Research compliance in healthcare requires structured oversight across the full clinical research lifecycle, including Medicare Coverage Analysis, study feasibility, billing review, documentation, and cross-functional governance. Healthcare organizations can reduce research compliance risk by defining ownership, integrating compliance early, standardizing documentation, and monitoring billing activity before errors escalate.
Clinical research plays a critical role in advancing patient care across hospitals, health systems, academic medical centers, and physician practices. As research activity continues to grow, so do regulatory expectations and enforcement scrutiny.
Recent developments in the National Institutes of Health (NIH) oversight landscape, updated Public Health Service (PHS) guidance, and new Office of Research Integrity (ORI) publications reflect increasing expectations for institutional accountability and structured oversight across the research lifecycle. At the same time, regulators have made clear that research-related activities, particularly those involving billing, financial relationships, and documentation, are definitely within the scope of healthcare fraud and abuse enforcement.
What are the biggest research compliance risks in healthcare?
Enforcement activity highlights consistent themes. Improper billing often stems from unclear ownership of decisions or weak internal controls, resulting in services being billed to federal programs that should have been covered by sponsors or not billed at all.
In many cases, these issues originate upstream, where organizations fail to perform a thorough Medicare Coverage Analysis (MCA) prior to clinical trial budget development. Without a well-documented MCA, organizations lack a defensible framework for determining which items and services qualify as standard of care versus research related, increasing the risk of duplicate billing, sponsor overpayments, or submission of non-billable services to federal programs.
Regulators also closely evaluate when issues are identified. When errors go undetected, financial exposure and remediation complexity increase.
Regulators are no longer focused on whether a program exists; they are focused on whether it works in practice. The Department of Justice (DOJ) and Office of Inspector General (OIG) assess compliance programs based on operational effectiveness, including whether controls actively prevent and detect improper billing, whether compliance functions are engaged in high-risk activities such as research, and whether issues are identified and addressed proactively.
Despite these expectations, research compliance—which focuses on processes, controls, and oversight activities designed to ensure that all research involving human subjects, data, or regulated products is conducted in accordance with applicable laws, regulations, ethical standards, and institutional requirements—is still often managed in silos or treated as a secondary consideration to an organization’s overall compliance program. Many organizations rely heavily on institutional review board (IRB) oversight or research administration processes, which, while foundational, are not designed to address the full spectrum of compliance risks tied to billing, financial relationships, or operational decision-making. As a result, research compliance has become a core component of an organization’s overall risk profile.
Five Research Compliance Challenges Organizations Often Overlook
Even organizations with established compliance programs encounter breakdowns in execution. These challenges are typically not due to a lack of awareness but rather gaps in how policies and processes are operationalized across the research lifecycle. The following areas reflect common patterns PYA has observed in practice, along with how organizations are addressing these risks.
1. Medicare Coverage Analysis (MCA) and Qualifying Clinical Trial (QCT) Determination
Why this Matters
An MCA, including a QCT determination when applicable, establishes the foundation for compliant research billing. It defines which services are billable to Medicare, sponsor-funded, or non-billable, and ensures alignment with applicable coverage and documentation requirements. Without a consistent MCA process, organizations lack a reliable roadmap for compliant claims submission.
Where Breakdowns Occur
In practice, MCA processes are often implemented inconsistently or too late in the research lifecycle. Organizations may complete MCAs after study initiation, rely on informal assessments, or assume coverage considerations were addressed through IRB review, despite those processes not being designed for billing compliance.
Supporting documentation may also be incomplete or fail to incorporate applicable Medicare coverage requirements, including National Coverage Determinations (NCDs), Local Coverage Determinations (LCDs), and clinical documentation standards. Incomplete documentation is a common root cause of improper billing identified in enforcement actions.
How To Address the Challenge
Leading organizations implement a standardized MCA/QCT process completed prior to study initiation, with clearly defined ownership, consistent templates, and integration of applicable coverage and documentation requirements. This approach ensures billing determinations are supported, consistent, and compliant before patient activity or billing begins.
2. Incomplete Study Feasibility Reviews
Why This Matters
Study feasibility reviews are a critical early checkpoint in the research lifecycle, but they often focus primarily on patient availability, investigator interest, and financial viability. Feasibility is not just about whether a study can be conducted; it is also about whether it can be conducted compliantly.
Where Breakdowns Occur
Many feasibility reviews do not fully assess whether existing systems and workflows can support compliant research billing and oversight. Key infrastructure, such as electronic medical record configuration, billing systems, coverage analysis tools, and sponsor payment tracking, may not be evaluated. As a result, studies often move forward without a clear plan for operationalizing billing and compliance requirements. These issues are frequently identified only after contracts are executed or patients are enrolled, when mitigation options are more limited. At that point, organizations are forced into reactive remediation rather than proactive risk mitigation.
How To Address the Challenge
Leading organizations incorporate compliance, billing, and research operations into feasibility reviews early in the process. This proactive measure ensures potential risks and operational limitations are identified, expectations are clarified, and mitigation strategies are implemented before studies are approved and initiated.
3. Limited Integration of the Research Compliance Function
Why This Matters
Effective research compliance requires coordination across multiple functions, including research operations, compliance, billing, and finance. Without alignment, critical decisions may be made in isolation. Fragmented oversight leads to inconsistent decision-making and increased risk exposure.
Where Breakdowns Occur
In many organizations, compliance involvement remains reactive, triggered only after issues emerge, audits identify concerns, or problems escalate. By the time compliance is engaged, studies are often already underway, and opportunities for early mitigation have passed. Additionally, the absence of formal governance structures, established communication pathways, and defined escalation processes can result in inconsistent handling of research-related compliance issues.
How To Address the Challenge
Leading organizations establish structured governance mechanisms, including cross-functional research compliance committees, defined roles and responsibilities, and routine research risk assessments. Proactive engagement throughout the research lifecycle enables earlier issue identification, stronger oversight, and more consistent decision-making.
4. Gaps in Research Compliance Documentation
Why This Matters
Documentation is essential to demonstrating compliance during audits and investigations. It provides evidence that decisions, billing determinations, and corrective actions were performed in accordance with applicable requirements. If an issue is not documented, it is difficult to demonstrate compliance, regardless of whether appropriate decisions were made.
Where Breakdowns Occur
Documentation remains a common and avoidable weakness. Organizations often rely on informal practices or incomplete records, resulting in gaps such as incomplete MCA files, undocumented billing calendars, insufficient justification for coverage determinations, and limited documentation of issue resolution. In these situations, organizations may be unable to substantiate compliance activities, increasing risk during regulatory review.
How To Address the Challenge
Leading organizations implement standardized documentation practices across the research lifecycle, including the use of consistent templates, centralized repositories, and clearly defined retention requirements. Documentation is structured to support billing decisions, compliance oversight, and corrective actions in a manner that withstands external scrutiny.
5. Lack of a Structured Research Billing Review Process
Why This Matters
Research billing is a high-risk area, yet processes often rely on informal knowledge or assumptions that systems will appropriately segregate charges. Without structured oversight, billing errors can occur undetected and lead to significant regulatory exposure.
Where Breakdowns Occur
Organizations frequently lack required pre-billing reviews, consistent application of billing calendars, and reconciliation processes between sponsor payments and patient billing activity. These gaps increase the risk of double billing, billing sponsor-funded services to federal programs, and submitting unsupported claims.
How To Address the Challenge
Leading organizations implement structured billing review processes that include mandatory pre-billing reviews, defined ownership of billing oversight, and ongoing monitoring and reconciliation activities between study budgets, billing calendars, and patient billing records. These controls enable early detection of errors and reduce the risk of improper claims submission.
Moving from Framework to Function
An effective research compliance program is no longer defined by the presence of policies or isolated controls. It is defined by how well those controls are integrated into day-to-day operations across the research lifecycle.
Organizations that succeed in this environment move beyond reactive compliance and embed oversight into the way research is operationalized, from feasibility through billing and ongoing monitoring. By addressing common operational gaps and strengthening coordination across functions, organizations can reduce risk, improve consistency, and better withstand increasing regulatory scrutiny, while supporting the integrity and sustainability of their research programs.
For more than 40 years, PYA has helped our healthcare clients build research compliance programs that withstand regulatory scrutiny.
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