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Rare Disease Pharmacy Insights

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Mar 27, 2025

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1. Executive summary

The United States rare disease treatment market is experiencing substantial growth, creating a dynamic landscape for specialty pharmacies that serve this unique patient population. 

This report analyzes the competitive dynamics between independent and national specialty pharmacies within this sector in 2025. Both types of pharmacies play a crucial role in providing specialized care and access to often complex and high-cost medications for individuals with rare diseases. 

Key competitive dynamics revolve around personalized care versus broader reach, agility versus established infrastructure, and the ability to navigate the intricate reimbursement and regulatory environment. 

While national pharmacies benefit from their scale and payer relationships, independent pharmacies often differentiate themselves through tailored patient support and deep expertise in specific rare conditions. External factors such as technological advancements, patient support program evolution, and shifting payer strategies are significantly influencing this competition.

The future landscape is expected to see continued growth and specialization, with both independent and national players adapting to meet the increasing demands of this complex market.

2. Introduction

The US specialty pharmacy market has become an integral component of the pharmaceutical industry, responsible for dispensing high-cost, complex medications that require specialized handling, administration, and patient monitoring. Within this market, the rare disease sector stands out due to the unique challenges associated with diagnosing and treating conditions that affect fewer than 200,000 Americans [1]. 

The increasing prevalence and awareness of rare diseases, coupled with advancements in therapeutic options, have led to significant growth in this area. 

This report focuses on the competitive landscape between two primary types of specialty pharmacies operating within the US rare disease market in 2025: independent and national.

Independent specialty pharmacies are typically smaller, privately-owned entities that may focus on specific disease states or patient populations. National specialty pharmacies, on the other hand, often have a broader geographic reach, greater resources, and are frequently affiliated with larger healthcare organizations such as Pharmacy Benefit Managers (PBMs) or insurance companies. 

Understanding the competitive interplay between these two types of pharmacies is crucial for pharmaceutical manufacturers, payers, healthcare providers, and, most importantly, the patients who rely on their services. 

This report aims to provide a comprehensive analysis of this competition in 2025, considering market share, competitive advantages, challenges, the impact of market events, and the influence of external factors.

3. The landscape of rare disease treatment and specialty pharmacies

3.1. Overview of the US rare disease treatment market

Market size and growth:

  • The US rare disease treatment market was valued at USD 76.93 billion in 2024 and is projected to reach approximately USD 184.68 billion by 2034, demonstrating a CAGR of 9.15% from 2025 to 2034 [1].


  • This growth trajectory presents significant opportunities for specialty pharmacies.

Global market overview:

  • The global rare disease treatment market was valued at USD 244.57 billion in 2025 and is forecast to grow to USD 527.05 billion by 2034, with a CAGR of 8.92% [1].

  • The North American region, led by the US, accounted for 49% of the global market revenue in 2024 [1].

Key market drivers:

  • Increasing proportion of overall drug spending attributed to specialty medications [2].

  • Specialty drugs are defined by their high cost, complex administration, and specialized patient management requirements.

  • By mid-2024, approximately 75% of new drugs under development were classified as specialty drugs [3].

Specialty drug market influence:

  • Specialty drugs are projected to account for over 50% of total US drug spending by 2025-2026 and beyond [2].

  • Their significant financial impact highlights the economic importance of specialty pharmacies in the rare disease sector.

Regulatory support and drug development:

  • The increasing number of orphan drug approvals by the FDA contributes significantly to market growth [4].

  • Growth is further supported by policies incentivizing accelerated development of treatments for rare conditions [4].

3.2. The critical role of specialty pharmacies in rare disease medications

Indispensable role in rare disease management :

  • Specialty pharmacies play a crucial role in managing rare diseases due to the complex nature of these conditions and their treatments. [5]

Specialized services and support :

Specialty pharmacies offer tailored services to meet the specific needs of rare disease patients, including:

  • Ensuring proper handling and storage of temperature-sensitive medications.

  • Providing detailed education on medication administration and potential side effects.

  • Offering comprehensive patient monitoring to enhance safety and efficacy. [3]

Complex medication management :

Specialty medications often require specialized management due to:

  • Specific administration methods like injections or infusions.

  • Significant side effect profiles that require careful monitoring.

  • Special access conditions mandated by manufacturers or payers, necessitating expert care and patient support.[6]

Comprehensive patient care:

Specialty pharmacies provide critical clinical management and product support services by:

  • Acting as a central point of contact for patients, caregivers, and healthcare providers.

  • Ensuring high-touch care models to improve patient adherence to demanding treatment regimens.

  • Managing medication dosing and potential adverse events to ensure safe and effective medication use. [7]

Growing market for advanced therapies :

  • The healthcare market is experiencing growth in the development and approval of rare and ultra-orphan treatments, as well as innovative cell and gene therapies. [8]

  • These advanced therapies often involve specific distribution, handling, and administration requirements, reinforcing the critical role specialty pharmacies play in ensuring access to and effective management of these cutting-edge treatments.

4. Analyzing the competitive dynamics

4.1. Market share and growth trajectories

Data challenges:

  • Obtaining precise, publicly available market share data specifically segmented by ownership type (independent vs. national) within the rare disease sector remains challenging.

  • Market reports often aggregate data at a broader level, either encompassing the entire specialty pharmacy market or focusing on specific therapeutic areas without clear segmentation.

PBM-affiliated pharmacies:

  • Pharmacies affiliated with Pharmacy Benefit Managers (PBMs), which are often national in scope, control a significant portion of the overall specialty pharmacy market. [9]

  • In 2022, three major PBMs accounted for nearly two-thirds of all prescription revenues from specialty drugs dispensed by pharmacies. [10]

  • This substantial market share suggests that national specialty pharmacies, particularly those integrated with PBMs and insurers, likely hold a considerable share within the rare disease market as well.

  • Vertical integration of PBMs with their own specialty pharmacies can create inherent advantages, potentially influencing dispensing patterns and market share through formulary management and

preferred network agreements. [9]

Market rankings:

  • Reports ranking top specialty pharmacies by revenue often include a mix of large national chains and some larger independent players. [11]

  • While these rankings may not focus exclusively on rare diseases, they provide insight into the relative size and influence of different entities within the specialty pharmacy landscape.

Growth and opportunities:

  • The overall specialty pharmacy market is experiencing significant growth, driven by: An increasing number of specialty medications and high costs associated with specialty drugs. [2]

  • This expansion creates opportunities for both independent and national pharmacies to grow their presence in the rare disease sector.

  • The increasing number of novel specialty drugs, including those for rare diseases, suggests a dynamic environment where both types of pharmacies are competing for market share.

4.2. Competitive strengths of independent specialty pharmacies

Personalized patient care and relationships:

  • Independent specialty pharmacies excel in offering personalized care and fostering strong connections with both patients and healthcare providers, which is vital in the rare disease community [4].

Patient-centric model:

  • Their smaller scale and focused approach enable a more patient-centric model, tailoring services to the unique and complex needs of individuals with rare conditions.

  • This model may include: Dedicated support, enhanced communication and deeper understanding of specific rare disease challenges

Specialization example: PANTHERx Rare Pharmacy

  • PANTHERx Rare Pharmacy has established itself by specializing in complex rare and orphan diseases.

  • They develop interdisciplinary “RxARECARE” teams dedicated to specific products, allowing their care teams to: Gain therapy-specific expertise and build stronger rapport with patients and healthcare providers [12]

Community engagement and local focus:

  • Independent specialty pharmacies' local presence enables: Better understanding of regional healthcare ecosystems, stronger ties with local physicians, patient advocacy groups, and community resources and enhanced comprehensive support for rare disease populations

Agility and flexibility:

  • Compared to larger national chains, independent specialty pharmacies demonstrate greater adaptability to:
    evolving rare disease patient needs and rapidly changing market conditions

  • They can implement new technologies and patient support programs more swiftly and tailor services to meet specific patient requirements.

Advocacy and education:

  • For niche therapies, independent specialty pharmacies can: Educate payers on the clinical and economic value of rare disease treatments and advocate for improved patient access [13]

Valuable Partnerships for Manufacturers:

  • With focused knowledge in rare conditions, these pharmacies can effectively support manufacturers in navigating complex reimbursement landscapes.

4.3. Competitive strengths of national specialty pharmacies

Broader geographic reach and extensive networks:

  • Serve patients across a wider geographic area, benefiting individuals in rural or underserved regions with limited access to local specialized care.

  • Robust mail-order capabilities further extend their reach. [4]

Established relationships with major insurance companies and PBMs:

  • Greater negotiating power due to their size and scale.

  • Potentially secure more favorable contract terms and preferred network status.

  • Enhanced formulary inclusion and improved reimbursement rates for rare disease medications. [4]

Financial resources and advanced infrastructure:

  • Access to substantial financial resources enables investments in advanced technologies for dispensing, data management, and patient support programs.

  • Dedicated teams specializing in regulatory compliance, data analytics, and patient assistance ensure efficient operations and comprehensive services. [4]

Integration with vertically integrated healthcare organizations:

  • Often part of PBMs, insurers, or large health systems, which can streamline processes and improve care coordination.

  • Integration can offer cost advantages and facilitate smoother prior authorizations and claims processing for rare disease medications. [14]

Competitive advantages of independent vs. national specialty pharmacies in the rare disease market

Independent pharmacies :

  • Personalized patient care and high-touch approach

  • Community focus and local expertise

  • Agility and flexibility

  • Potential for specialized payer education for niche therapies

National Pharmacies: 

  • Broader geographic reach and extensive networks

  • Established relationships with payers and negotiating power

  • Greater resources and infrastructure

  • Integrated services within larger healthcare organizations

5. Challenges and obstacles in the rare disease market

5.1. Challenges faced by independent specialty pharmacies

Contract negotiation challenges:

  • Independent specialty pharmacies often struggle to secure favorable contracts with large payers.

  • Gaining access to preferred pharmacy networks is challenging, limiting patient access to their services. [15]

Disadvantage compared to national chains:

  • Their smaller size and lower prescription volume place them at a disadvantage in negotiations with major insurance companies and PBMs.

  • Larger networks are often prioritized for cost management and administrative efficiency. [15]

Limited distribution drugs (LDDs) access:

  • Independent pharmacies face hurdles in accessing LDDs for rare diseases.

  • Manufacturers frequently choose to distribute rare disease medications through select specialty pharmacy networks, often favoring larger national players with established infrastructure and

broader reach.

  • This restricted access can prevent independent pharmacies from serving patients with specific rare conditions, despite possessing the necessary expertise and care capabilities. [15]

Cost pressures and declining reimbursement rates:

  • Smaller independent pharmacies, operating with tighter profit margins, are disproportionately impacted by increasing cost pressures and reduced reimbursement rates from payers. [15]

Complex reimbursement process:

  • Managing reimbursement for high-cost rare disease drugs is complex.

  • Independent pharmacies may struggle with prior authorizations and potential denials due to limited administrative resources. [15]

Impact of direct and indirect remuneration (DIR) fees:

  • DIR fees, often applied retroactively by payers and PBMs, can further erode independent pharmacy profitability, posing challenges in remaining competitive. [15]

Technology and data management barriers:

  • Independent pharmacies may face difficulties investing in and maintaining sophisticated technology systems.

  • Such systems are crucial for handling rare disease therapies and meeting the stringent reporting requirements set by manufacturers and payers.

  • National pharmacies, with greater financial resources, often have an advantage in implementing these essential tools. [10]

5.2. Challenges faced by national specialty pharmacies

Personalized care challenges:

  • National specialty pharmacies may struggle to maintain the same level of personalized care that independent pharmacies provide, especially when serving a large and geographically dispersed patient population [12].

  • Larger organizations' focus on standardization and efficiency might reduce individualized patient support, which is crucial for individuals with complex rare diseases.

Potential conflicts of interest:

  • National specialty pharmacies owned by or affiliated with PBMs or insurers may face potential conflicts of interest [9].

  • Concerns exist about PBMs steering patients towards their own affiliated pharmacies, which could influence formulary decisions or restrict patient choice, potentially not aligning with the patient's best interest.

Regulatory and licensing challenges:

  • Operating across multiple states requires navigating complex state regulations and licensing requirements.

  • Each state has distinct pharmacy laws and regulations, increasing administrative complexity.

Staff training and knowledge maintenance:

  • National specialty pharmacies must consistently update their large networks and staff on advancements in rare disease treatments and clinical guidelines [16].

  • The rare disease landscape evolves rapidly with new therapies and diagnostic tools, necessitating ongoing staff training to provide effective and up-to-date care.

Key challenges faced by independent vs. national specialty pharmacies in the rare disease market

Independent pharmacies:

  • Negotiating with payers and access to preferred networks

  • Access to limited distribution drugs (LDDs)

  • Reimbursement complexities and cost pressures

  • Technological investments and data management

National pharmacies:

  • Maintaining personalized care at scale

  • Potential for conflicts of interest within larger organizations

  • Navigating regulatory hurdles and compliance across multiple states

  • Adapting to a rapidly evolving treatment landscape

6. The impact of market events and external factors

6.1. Mergers, acquisitions, and partnerships

The healthcare and pharmaceutical sectors have seen significant merger and acquisition (M&A) activity, impacting the competitive landscape of specialty pharmacies, particularly those focusing on rare diseases. 

Industry consolidation can:

  • Increase market share for larger entities.

  • Create challenges for smaller independent pharmacies.

Examples of notable activities:

  • Elevance Health has entered the top 15 US pharmacies for the first time due to strategic acquisitions and the launch of its own mail pharmacy, showcasing the trend of insurers expanding their pharmacy operations [20].

  • The potential acquisition of Walgreens Boots Alliance by Sycamore Partners could significantly reshape the retail pharmacy landscape and impact specialty pharmacy services [14].

In the rare disease therapeutic space:

  • Pharmaceutical companies are increasingly acquiring or partnering with biotech firms that are developing innovative treatments [1].

  • While these deals may not directly involve pharmacies, they heavily influence the pipeline of rare disease treatments that specialty pharmacies will eventually dispense.

Notable transactions include:

  • AstraZeneca's acquisition of Amolyt Pharma [17].

  • Vertex Pharmaceuticals' purchase of Alpine Immune Sciences [17].

These activities reflect strong investment and interest in the rare disease market, driving demand for specialized pharmacy services.

Another significant transaction is Clayton, Dubilier & Rice's acquisition of Sanofi's consumer health business Opella, expected to close in 2025, signaling continued investment in the broader healthcare sector [18].

6.2. Technological influences

Digital platforms for patient engagement:

  • Enhances communication between patients, providers, and payers.

  • Supports improved medication adherence and time-to-fill rate insights [10]

Data analytics for personalized care:

  • Facilitates tailored treatment strategies based on individual patient data.

  • Helps uncover trends in medication adherence and optimize treatment outcomes [16].

Electronic health records (EHR) for improved care coordination:

  • Enhances collaboration between healthcare providers.

  • Streamlines information sharing for better patient management [16].

Challenges with current electronic prescribing platforms:

  • Often lack the capability to capture detailed data such as patient weight or genetic test results.

  • Reliance on outdated methods like faxing prescriptions and clinical documentation persists [19].

Advancements in technology to improve efficiency:

  • The development of enhanced digital tools is crucial to meet complex data requirements.

  • Improved platforms can reduce delays in therapy initiation and improve operational processes.

Importance of real-world data (RWD) and analytics:

  • Enables specialty pharmacies to gain insights into patient journeys.

  • Helps identify potential barriers to adherence.

  • Demonstrates value to payers and manufacturers by improving patient outcomes and cost-effectiveness [16].

6.3. The role of patient support programs

Importance of patient support programs:

  • Comprehensive support programs are vital for improving patient outcomes and satisfaction in the rare disease market. These programs significantly influence a patient's choice of specialty pharmacy. [4]

Support services offered by specialty pharmacies:

  • Financial assistance programs help patients manage the high costs of rare disease medications.

  • Educational resources improve patient understanding of their condition and treatment.

  • Adherence programs promote compliance with medication regimens.

Specialty pharmacy roles:

  • Provide training on proper medication use.

  • Conduct comprehensive treatment assessments.

  • Closely monitor patients for side effects and efficacy.

  • Maintain regular communication with caregivers and prescribing physicians. [7]

Financial support importance:

  • Due to substantial out-of-pocket costs for rare disease medications, financial support programs are essential. [7]

  • Effective connections with financial assistance programs (offered by manufacturers, non-profits, or advocacy groups) provide significant value and a competitive edge for pharmacies.

  • Without adequate support, high costs may lead to medication abandonment, negatively impacting patient health outcomes and the healthcare system.

Robust financial support programs are crucial for ensuring medication adherence and treatment success in the rare disease population.

6.4. Payer strategies and reimbursement models

Payer strategies impact on specialty pharmacy competition:

  • Payers implement strategies such as prior authorizations, formulary restrictions, and site-of-care policies, which significantly influence competition between independent and national specialty pharmacies in the rare disease market [6].

  • These strategies are designed to manage the high costs of specialty drugs, including those for rare diseases.

  • Payers’ decisions can significantly affect patient access to medications and preferred pharmacy channels.

  • Pharmacies that are part of a payer’s network or excel in navigating complex prior authorization processes often gain a competitive advantage.

Emphasis on value-based care and outcomes-based reimbursement models:

  • The healthcare industry is shifting towards value-based care and outcomes-based reimbursement models [6].

  • Specialty pharmacies are now expected to demonstrate not only their ability to dispense medications but also their role in achieving positive patient outcomes.

  • Pharmacies that effectively collect and report data showcasing improved patient health, medication adherence, and overall cost savings are better positioned for success in this evolving landscape.

  • Payers are increasingly evaluating specialty pharmacies based on the overall value they provide in managing complex conditions like rare diseases.

Site-of-care policies and their impact:

  • Payers are actively implementing site-of-care policies to direct the administration of infused medications to lower-cost settings, such as ambulatory infusion centers [8].

  • This trend may influence the dispensing volume of specialty pharmacies handling certain rare disease therapies that require infusion.

7. Strategies for independent specialty pharmacies to win contracts:

Independent specialty pharmacies can differentiate themselves and win contracts in the competitive rare disease market by focusing on several key strategies:

  • Develop deep expertise in specific rare diseases: By concentrating on a limited number of rare conditions, independent pharmacies can cultivate in-depth knowledge of the disease, its treatment protocols, and the specific needs of patients [6]. This specialization allows them to build interdisciplinary teams with therapy-specific expertise, fostering strong relationships with both patients and healthcare providers [20]

  • Offer highly personalized and patient-centric care: Independent pharmacies can emphasize a high-touch model of care, providing individualized support, enhanced communication, and a comprehensive understanding of the unique challenges faced by rare disease patients [20]. This includes offering services such as training on medication use, comprehensive treatment assessments, patient monitoring, and frequent communication with caregivers and physicians. [20,21]

  • Excel in navigating the complex reimbursement landscape: They can leverage their expertise to assist patients with benefits investigations, co-pay assistance, and prior authorization support, which are critical for accessing often costly rare disease medications [20,21]. Independent pharmacies can also educate payers about the clinical and economic value of novel rare disease treatments [21,23].


  • Build strong relationships with local healthcare providers and patient advocacy groups: By embedding themselves in local communities, independent pharmacies can foster stronger ties with physicians and patient organizations. [24] This allows for better coordination of care and a deeper understanding of the specific needs of the patient population they serve [20].

  • Demonstrate agility and flexibility: Compared to larger national chains, independent pharmacies can often adapt more quickly to the evolving needs of rare disease patients and the rapidly changing market [20]. This nimbleness can be a significant advantage in implementing new technologies and patient support programs.

  • Leverage data and technology for enhanced outcomes: By utilizing digital tools and data analytics, independent pharmacies can gain deeper insights into patient journeys, track medication adherence, and identify potential barriers to treatment [22,25]. This data can be used to demonstrate their value to payers and manufacturers through improved patient outcomes and cost-effectiveness [22].

  • Obtain rare Disease specific certifications: Achieving certifications like the URAC Rare Disease Certification can signal a commitment to quality and specialized expertise in managing rare disease therapies. [24,25]. This can be a key differentiator when seeking contracts with manufacturers and payers.

  • Focus on limited distribution drugs (LDDs): By specializing in handling and dispensing LDDs for rare diseases, independent pharmacies can become preferred partners for manufacturers who often select a limited network of pharmacies for these specialized medications [24,26]


  • Offer Comprehensive Patient Support Programs: Developing robust patient support programs that go beyond dispensing, including financial assistance, educational resources, and adherence programs, can significantly enhance patient satisfaction and outcomes, making the pharmacy more attractive to both patients and prescribers [20].

By focusing on these areas, independent specialty pharmacies can highlight their unique value proposition and successfully compete for contracts in the growing and complex rare disease market.

8. Future outlook and predictions for 2025

Growth outlook:

  • The rare disease treatment market and specialty pharmacy sector are projected to maintain strong growth through 2025 and beyond, sustaining a competitive environment for both independent and national specialty pharmacies. [1]

National specialty pharmacies:

  • National specialty pharmacies integrated with PBMs and insurers are expected to retain a significant market share due to: Established payer relationships, extensive resources, broad geographic reach [9], financial incentives for PBMs to prioritize their own specialty pharmacy operations will likely continue, reinforcing their dominance. [9]

Independent specialty pharmacies:

  • Independent specialty pharmacies will focus on niche areas within the rare disease market by:Emphasizing personalized patient care, building strong relationships with patients and prescribers,leveraging agility to differentiate themselves [13], specializing in specific rare conditions and offering high-touch service models will be key strategies for success. [13]

Technology and data analytics:

  • Effective use of technology and data analytics will become increasingly vital in enhancing: Patient outcomes, Operational efficiency and compliance with payer and manufacturer reporting requirements [16]

Cost pressures and value demonstration:

  • Specialty pharmacies must focus on demonstrating value through improved patient outcomes and efficient care management to address rising cost pressures from payers. [6]

  • The high costs of rare disease treatments will continue to prompt scrutiny from payers and policymakers. [6]

Cell and gene therapy management:

  • The growing number of cell and gene therapies entering the market will require specialized expertise in: Storage, administration and patient monitoring [8]

Regulatory and policy changes:

  • Shifts in drug pricing regulations, orphan drug incentives, or PBM practices could significantly impact the strategies and profitability of both independent and national specialty pharmacies. [17]

9. Conclusion

The competitive landscape between independent and national specialty pharmacies in the US rare disease market in 2025 is characterized by a dynamic interplay of strengths and challenges. 

National pharmacies benefit from their scale, payer relationships, and extensive resources, allowing them to capture a significant market share. However, independent pharmacies carve out a competitive niche by offering personalized, high-touch care, often specializing in specific rare conditions and fostering strong community ties. 

External factors such as technological advancements, the evolution of patient support programs, and shifting payer strategies are significantly influencing this competition, requiring both types of pharmacies to adapt and innovate. 

The continued growth of the rare disease treatment market presents opportunities for all players, but success will depend on the ability to navigate the complex reimbursement and regulatory environment, leverage technology effectively, and ultimately meet the unique and evolving needs of the rare disease patient population.

References

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