Clinical Trial Budgeting and Contract Negotiation

Every clinical trial budget tells a financial story, and the first session of this workshop teaches participants how to read that story critically and construct their own narrative with precision. The session begins with the anatomy of a clinical trial budget, breaking down the three fundamental cost categories that every site must account for: per-patient costs (visit-level procedures, assessments, and coordinator time that scale with enrollment), fixed costs (startup activities, regulatory submissions, IRB fees, and closeout procedures that occur regardless of enrollment volume), and pass-through costs (central lab kits, shipping, investigational product storage, and other expenses that the site incurs on behalf of the sponsor and should recover at cost or with a handling margin).

Participants will learn to deconstruct sponsor budget templates — understanding why sponsors structure their budgets the way they do and identifying where sponsor templates systematically undervalue site effort. Common areas of undervaluation include unscheduled visit management, screen failure processing costs, query resolution time, source document preparation, and the administrative overhead of regulatory maintenance throughout the study lifecycle. The session provides a detailed methodology for calculating true per-visit costs, including direct procedure costs, coordinator time allocation based on protocol complexity metrics, PI oversight time, and institutional overhead rates.

Industry benchmarking data is presented to give participants concrete reference points for evaluating sponsor budget proposals. Participants will review aggregated data on per-patient payment ranges across major therapeutic areas — oncology, cardiology, neurology, rare disease, and healthy volunteer studies — and learn how factors such as protocol complexity, visit frequency, procedure intensity, and data collection burden should influence the per-patient rate a site targets during negotiation. The session also covers overhead calculation methodologies, including how to determine an appropriate indirect cost rate that captures the true institutional burden of hosting clinical research without exceeding defensible limits.

Fair market value is not merely a financial concept — it is a compliance requirement with serious legal implications. The Anti-Kickback Statute (AKS) and the False Claims Act create a regulatory environment in which payments between sponsors and investigative sites must reflect the fair market value of the services actually rendered. Payments that exceed FMV can be construed as inducements for referrals, while payments below FMV may indicate that a site is subsidizing sponsor costs in exchange for other benefits. This session provides a rigorous framework for establishing, documenting, and defending FMV rates at your site.

Participants will learn the core principles of FMV determination as applied to clinical research — including how to establish hourly rates for coordinator time, PI time, and sub-investigator time that reflect local market conditions, experience levels, and the specific demands of clinical trial work versus standard clinical care. The session covers how to value common clinical trial procedures using a combination of Medicare fee schedule benchmarking, institutional chargemaster rates, and published FMV survey data from organizations such as ACRP and industry compensation surveys. Particular attention is given to valuing procedures and activities that do not have direct clinical equivalents, such as informed consent discussions, source document completion, query resolution, and regulatory file maintenance.

Documentation requirements for FMV compliance are covered in detail, because having a defensible rate is only half the equation — you must also be able to demonstrate how that rate was determined. Participants will learn to create and maintain FMV documentation packages that include the methodology used, the data sources consulted, the date of the analysis, and the rationale for the final rate selected. The session addresses common FMV pitfalls, including applying a single blanket rate across all studies regardless of complexity, failing to update FMV analyses on a regular cycle, using compensation data from unrelated geographic markets, and neglecting to account for the difference between billable and non-billable coordinator activities. AKS safe harbor provisions relevant to research site payments are reviewed to help participants understand the legal boundaries within which their FMV rates must fall.

For any site that treats Medicare beneficiaries — which includes the vast majority of clinical research sites in the United States — Medicare coverage analysis (MCA) is not optional. The failure to properly identify which costs in a clinical trial are billable to Medicare, which must be billed to the sponsor, and which are the site’s responsibility can result in false claims liability under the False Claims Act, which carries penalties of up to three times the amount of the false claim plus per-claim fines. This session provides site leadership with the foundational knowledge to ensure their billing practices are compliant.

The session begins with the CMS Clinical Trial Policy (National Coverage Determination 310.1), which establishes the framework for Medicare coverage of routine costs in qualifying clinical trials. Participants will learn the specific criteria that define a qualifying trial — including trials funded by NIH, CDC, AHRQ, CMS, DOD, or VA; trials conducted under an FDA IND or IDE; and trials exempt from IND/IDE requirements that meet certain additional criteria. The critical distinction between routine costs and research costs is examined in detail: routine costs include items and services that would be provided to the patient regardless of trial participation (standard-of-care procedures, monitoring, and management of side effects), while research costs include the investigational item or service itself, items provided solely for data collection purposes, and services that are clearly required only by the research protocol.

Participants will work through practical MCA scenarios using realistic protocol excerpts, identifying line items that are billable to Medicare as routine care, items that must be billed to the sponsor as research costs, and items that fall into the gray area requiring clinical judgment and institutional policy guidance. The session covers the role of the MCA in the budget negotiation process — because the outcome of the coverage analysis directly affects which costs the sponsor must cover, which the site can bill to insurance, and which represent a potential financial gap that the site must either negotiate to close or absorb. Common billing compliance failures are reviewed, including billing Medicare for protocol-required procedures that have no clinical indication, failing to identify research-only imaging or laboratory studies, and improperly routing charges through the institutional billing system without proper research flags.

The clinical trial agreement (CTA) is the single most important document governing the financial and legal relationship between a site and a sponsor, yet many sites treat contract review as a formality rather than a strategic negotiation opportunity. This session transforms participants from passive contract recipients into informed negotiators who understand which terms matter most, where the leverage points are, and how to advocate for their site’s interests without derailing the study startup timeline.

The session begins with a systematic review of key contract terms that directly impact site financial performance and risk exposure. Indemnification clauses are examined in detail — participants learn to distinguish between acceptable mutual indemnification provisions and one-sided indemnification language that exposes the site to liability for sponsor-caused injuries. Intellectual property provisions are reviewed with attention to ownership of data generated at the site, restrictions on use of study results, and the implications of IP assignment clauses that some sponsors embed in standard contract templates. Publication rights are critically important for academic sites, and participants learn to identify and negotiate restrictions on publication timing, sponsor review periods, and the right to publish site-specific results independently of the sponsor’s controlled publication strategy.

Termination clauses represent one of the highest-risk areas of any clinical trial agreement. Participants will learn to evaluate termination provisions for fairness, including whether the sponsor can terminate without cause with insufficient notice, whether the site is entitled to payment for work completed prior to termination, how enrolled patients will be managed during a wind-down period, and whether the site retains the right to terminate if the sponsor fails to meet its own obligations. Payment terms are reviewed with attention to invoicing procedures, payment timelines (Net 30 vs. Net 45 vs. Net 60), currency and wire transfer specifications, milestone-based versus enrollment-based payment schedules, and the financial impact of slow-paying sponsors on site cash flow.

The session concludes with practical negotiation strategy, including how to identify red flags that indicate a contract requires significant revision, how to prioritize negotiation points when you cannot win on every term, how to use competing study opportunities as leverage without damaging sponsor relationships, and how to document negotiation outcomes in contract amendment language that is clear and enforceable. Participants will review a sample contract with annotated red flags and practice drafting redline responses to problematic clauses, building the confidence and specificity needed to negotiate effectively with sponsor legal teams and CRO contract administrators.