Baker Donelson serves academic medicine organizations operating at the intersection of clinical care, education, and research. We advise academic medical centers, teaching hospitals, medical schools, faculty practice plans, and affiliated entities on the legal and operational issues that come with complex mission driven structures and high expectations from regulators, payors, and the communities they serve.
Academic medicine rarely exists within a single organizational structure. More often, it is a network of entities with shared goals and different incentives, including universities, health systems, medical groups, and external clinical partners. We help leadership teams align those interests, document relationships clearly, and build durable structures that support the mission, protect the brand, and work in real life.
Structuring affiliations that work in practice
Academic medicine depends on affiliations. The relationships among medical schools, teaching hospitals, faculty practice plans, and health systems are complex, long term operating models. To be successful, they must clearly allocate authority, support mission-critical work, protect academic priorities, and enable effective decision-making throughout the life of the partnership. These affiliations must also account for a central tension: the need to collaborate closely around a shared mission while preserving each institution's independence in governance, finances, operations, and competitive strategy.
We help clients design, negotiate, revise, and implement affiliation structures that work in practice, not just on paper. Drawing on our deep experience with academic medical centers, independent colleges of medicine, teaching hospitals, faculty practice plans, and affiliated health systems, we work with clients to anticipate where relationships may be tested and build structures that can adapt as leadership, strategy, regulatory requirements, and market conditions change.
Our work includes:
- Hospital, health system, and university affiliation agreements, including governance, branding, academic authority, clinical and research strategy, and decision rights;
- Master affiliation agreements and related operating documents that translate broad strategic commitments into day-to-day responsibilities;
- Funds flow and financial support arrangements tied to clinical, teaching, and research missions;
- Professional services, faculty practice plans, and physician alignment arrangements that reflect the realities of academic practice and comply with applicable regulatory requirements;
- Service line and clinical program affiliations that extend to specialty services, support workforce development, and preserve training and academic objectives;
- Antitrust and contracting, fraud and abuse, tax-exempt, and governance considerations where affiliated organizations collaborate clinically or academically while remaining legally distinct and, at times, competitively sensitive.
We regularly represent health systems that serve as teaching hospitals for independent colleges of medicine. These models can be highly effective, but only when the affiliation terms are clear on how to protect the faculty and training pipelines, structure funds flow that both institutions can defend to their own boards and auditors and build governance structures that function long after signing the documents. Our role is to get the structure right at formation and to guide our clients as the affiliation evolves through leadership transitions, mission shifts, and the negotiations that inevitably follow.
Graduate medical education, reimbursement, and teaching operations
Teaching hospitals and academic health systems must consider complex reimbursement requirements and regulations that extend beyond standard hospital reimbursement. Understanding graduate medical education (GME) payment rules is not only a reimbursement matter, but also a workforce strategy, a compliance obligation, and the foundation for developing a sustainable physician workforce in the communities that academic medical centers serve. Navigating Medicare GME payments is critical when providers establish and expand residency programs.
Our team can provide comprehensive guidance on the regulations that govern GME cap-building and setting per resident amounts (PRAs). Our team is well-positioned to counsel on the strategic planning, pro forma considerations, and funds flow agreements that are necessary in the initial stages of GME growth and expansion because the payment implications when establishing a new teaching hospital are significant and permanent. We also serve our clients' GME needs in numerous other ways, including but not limited to the following:
- Assessing GME expansion opportunities including applying for cap distributions as well as federal and state medical education, teaching health center grants, and Rural Health Transformation Program workforce development funds;
- Providing due diligence support for transactions involving teaching hospitals;
- Identifying community support and redistribution issues that could deter GME payment;
- Advising on regulatory requirements pertaining to operating nursing and allied health programs;
- Identifying regulatory and mission support considerations arising out of affiliation agreements and renegotiating these agreements to ensure compliance;
- Navigating the payment rules related to establishing new teaching hospitals or rural training track programs;
- Interpreting the regulations related to closing teaching hospitals and programs, including how to apply for temporary transfers of GME cap slots for displaced residents and Section 5506 redistributions from closed hospitals;
- Advising on teaching physician billing rules and moonlighting requirements, drafting policies to comply with applicable requirements, and representing clients in enforcement actions arising from alleged failures to comply with these rules;
- Providing guidance on the GME implications of rural reclassification while also considering other wage index and payment impacts;
- Representing hospitals in Provider Reimbursement Review Board (PRRB) appeals focusing upon issues arising out of GME cap and cost report audits.
Our team brings both technical fluency in GME payment rules and hands-on experience with the regulatory compliance and operational challenges that define academic medicine in practice.
Faculty practice plans and physician alignment
Faculty practice plans can be the engine that sustains clinical access, teaching capacity, and research growth, but they also introduce unique challenges. We support clients with:
- Formation, restructuring, and governance of faculty practice plans;
- Physician employment, contracting, compensation models, and fair market value support;
- Medical staff and leadership structures, including bylaws and peer review considerations;
- Arrangements with affiliated academic medical centers;
- Fraud and abuse, including Physician Self-Referral Law and Anti-Kickback statute compliance;
- Regulatory compliance issues that arise in academic compensation and mission-based subsidies.
Research, innovation, and technology transfer
Academic medical centers and universities are at the forefront of biomedical innovation, balancing research advancement with regulatory oversight, patient protection, and institutional risk management. We partner with research institutions to strengthen clinical research infrastructure, accelerate study activation, and safeguard institutional integrity. Our capabilities include:
- Clinical trial agreements and Food and Drug Administration (FDA) regulatory alignment, including indemnification, subject injury coverage, publication rights, research data use, and IP allocation;
- Privacy and data governance strategy for research, collaboration, and innovation, including HIPAA, General Data Protection Regulation (GDPR), cross-border data transfers, and AI-enabled research technologies;
- Human subjects' protection and Institutional Review Board (IRB) compliance, including informed consent development, single-IRB arrangements, reliance agreements, exemption and expedited review guidance, and risk assessments;
- Research integrity and grant compliance, including conflicts of interest, Bayh-Dole obligations, export controls, and foreign influence safeguards;
- Technology transfer, commercialization, and material transfer agreements, including policies governing biologics and research materials;
- Artificial intelligence (AI)-enabled research governance, including contracting support for AI-driven study recruitment solutions, clinical operations, and digital health technologies;
- FDA regulatory classification guidance for clinical decision support software and software as a medical device, including the four-criteria framework for non-device CDS and risk categorization for AI/ML-enabled clinical tools.
The broader academic medicine ecosystem
Academic medicine frequently includes affiliated programs that sit adjacent to the traditional medical school and hospital structure. We help organizations structure and manage these relationships, including:
- Affiliations involving colleges of nursing, colleges of pharmacy, and allied health programs;
- Clinical placement and training agreements, including supervision and liability allocation;
- Workforce development relationships with community partners and educational institutions;
- Health system sponsored health care academies designed to build local talent pipelines.
These relationships often create the most practical growth opportunities, especially in regions where academic medicine is not fully consolidated and partnerships can be built thoughtfully rather than inherited.
Governance, investigations, and institutional risk
Academic medicine leaders manage issues that touch employment, compliance, and institutional reputation. We support boards and executive teams with:
- Governance counseling and board-level decision support;
- Title IX and Title VII issues that arise in clinical and training environments;
- Internal investigations, dispute strategy, and crisis response;
- Policies, training, and practical process design for complex academic workplaces.