Joint Clinical Trials Office

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Budget Development and Cost

The JCTO is available to assist the PI and study team in the development of clinical trial budgets that meet the financial needs for study conduct. The first step in developing a comprehensive clinical trial budget is to perform an internal cost analysis. The cost analysis identifies all of the individual costs associated with a clinical trial, including evaluating standard of care procedures and staffing needs.

What is the difference between Budget Development and Budget Negotiation?

Budget development is the process of identifying all of the expenses associated with participating in a clinical trial.

Budget negotiation is the process of engaging the sponsor in a dialogue that results in a final budget that covers the costs of participating in a clinical trial.  Additional information on budget negotiations can be found here

Budget Development

The budget development process begins when an investigator is invited to participate in a clinical trial or when he/she decides to initiate a clinical trial and approach a sponsor for funding. In general, when a sponsor is initiating a clinical trial, a draft budget proposal will be provided with the start-up documents or within the draft CTA.

Type of budget received from sponsor JCTO budget development methodology
Flat per visit or per subject payment Create detailed internal budget using Schedule of Assessments, and WCM & NYP Charge-Masters
Detailed per subject payment Modify sponsor budget using Schedule of Assessments, and WCM & NYP Charge-Masters


It is important to take the time to identify costs before reviewing the sponsor's proposed budget so that the numbers presented do not influence the initial cost assessment. During this process, the JCTO or study team will also evaluate each study procedure to identify those that are standard of care and those being performed for research purposes only.

What resources do I need to develop a budget? Where do I get them?
Schedule of Assessments  Included in the Protocol
Standard Institutional Fees See Standard Fees Below
Evaluation and Procedure Charges, including CPT codes
Staff Allocation and Hourly Rates PI and Study Team

Budget line items

Indirect Cost Rate (IDC)

The WCM/NYP indirect cost rate of 35% applies to all procedural and non-procedural line items, as well as, to items that must be invoiced. The only items that may be exempt from IDC are those commonly identified as "pass-through" line items, such as subject stipends/reimbursements. IDC must be applied to each line item on the budget except the items listed below and pass-through costs.

  • Initial IRB Review: upon initial submission and review of the protocol by the IRB
  • IRB Amendment: upon sponsor-initiated amendment of the protocol
  • IRB Renewal: upon each annual continuing review of the protocol
  • JCTO: contract administration, management and negotiations

For more information on IDC, please scroll down.

Non-refundable startup fees

  • Clinical Study Evaluation Committee (CSEC)
  • IND Safety Reporting: to submit all IND Safety Reports for the duration of study
  • PI eCRF Training: for the investigator's time to learn sponsor's eCRF system 
  • Monitoring space: to offset rent expense on monitoring space
  • Recruitment: to promote subject enrollment 
  • Record Retention: to archive all research records for the required period of time 
  • Radiology start-up
  • Pharmacy (start-up and close-out)

Items requiring an invoice (not included in the per subject payment)

  • Non-procedural fees the sponsor has agreed to reimburse per the terms of the contract. (for example: subject travel, dry ice.)
  • Procedural assessments that do not pertain to every subject enrolled or may be considered optional per the study.

Note that when invoicing for these items the institution's indirect cost rate must be included.

Financial terms for consideration

  • Per subject payment withholding: Industry sponsors typically withhold a percentage of study payments until the study is completed. The percent withheld is usually 10% or greater. The withholding rate should be negotiated down to a minimum if possible.

  • Advances against subject payment (enrollment-based): The acceptance of advance payments for subject enrollment should be weighed carefully. If no subjects are enrolled the money will have to be refunded to the sponsor.

  • Non-refundable start-up fees: Sponsors may agree to provide payment of non-refundable start-up fees after the contract is fully executed, and in rare cases, even if the contract is not executed due to withdrawal of the study by the sponsor. There are some sponsors that include stipulations such as receipt of all regulatory documents, IRB approval and/or site initiation visit. Review these terms carefully and decide if they are acceptable.

  • Payment frequency: It is important to pay close attention to how often the sponsor will pay the institution. Payments may be based on: CRF completion/monitoring; a milestone number of subjects enrolled; completed study visits; additionally these payments may be made on a quarterly, monthly, etc. basis and some payments may be paid automatically, while others will require invoicing. A higher frequency of payments is desirable.

  • Per subject payments vs. items to be invoiced: Per subject payments include costs associated with each subject on each visit and they are often generated by the submission of CRFs to the sponsor. Items that require invoicing are those which may or may not be incurred depending on the subject's individual needs. Items that require invoicing should be clearly identified in the CTA budget exhibits.

  • Standard of Care vs. research only: It must be determined which services are standard of care (billable to the subject's insurance) and which services are billable to the study so that they can be appropriately incorporated in the budget and billing compliance plan.

  • Price capping: Price capping is not desirable. Price caps on devices expose the institution to substantial financial risk and should be negotiated out of the budget.

  • Screen failures: Sponsors prefer to pay a flat fee for screen failures rather than paying for actual costs incurred. Compensation for actual costs incurred is preferable.

  • IRB fees: Pay attention to terms that limit the number of IRB amendments and renewals that can be invoiced. These limits should be negotiated out of the budget.

For inquires contact


Fee Type

Fee Amount

Fee Required

Exempt From Fee




Industry-Sponsored (initiated and funded by industry)

Investigator-Initiated and Funded by a Federally Supported Research Center (e.g. CTSC)

Funded by a Private Foundation or Federal Grant Investigator-Initiated and Industry-Funded


The Joint Clinical Trials Office provides comprehensive oversight of clinical trial agreements and many other types of legal agreements. Indirect cost recovery offsets a portion of the on-going management costs, but does not fund the substantial front-end investment made in negotiating clinical trial agreements and setting up clinical trial accounts. The one-time JCTO administrative management fee partially offsets the following costs:

  • Contract review, negotiation and execution
  • Financial accuracy and feasibility review
  • Monitoring and electronic storage of legal agreements
  • Invoicing and accounts receivable management of initial set up costs
  • Compliance with applicable institutional and legal requirements
  • Quality control and industry sponsor relationship management


Industry-Sponsored (initiated and funded by industry)

The Clinical Study Evaluation Committee (CSEC) is a scientific and feasibility review committee. All clinical research protocols require review and approval by the committee prior to submission to the Institutional Review Board (IRB). The committee provides bio-statistical and bioethics resources to physician researchers. The committee consists of a multidisciplinary team of physicians, biostatisticians, pharmacists, and other health professionals.



IRB Fees

Fee Type

Fee Amount

Fee Required

Exempt from Fee




Industry Sponsored (initiated and funded by Industry)


Funded by private foundation, federal grant, or investigator – initiated


$1250 per year


$750 per amendment

Local Context Review

$1500 (Initial);
$1000 (Continuing Review)


Investigational Pharmacy Fees

Fee Type

Fee Amount

Fee Required

Contact JCTO for Guidance


Initial Investigational  Pharmacy Fee

$3375.00 (inclusive of IDC)

Industry-Sponsored (initiated and funded by industry)

Investigator-Initiated and Funded by a Federally Supported Research Center (e.g. CTSC)


Funded by a Private Foundation or Federal Grant Investigator-Initiated and Industry-Funded


This is a one-time fee that includes study initiation and closing costs.  The fee reimburses the investigational pharmacy for the time that is required of the pharmacist (PharmD) and/or pharmacy technician (PT) to perform non-dispensing related tasks included but not limited to:

  • Site qualification visit and site initiation visit
  • Review of the protocol prior to pharmacy approval and assessing feasibility
  • Reading the pharmacy manual and preparing the Protocol data sheet for IDS use
  • IT work up to upload the study
  • Meeting with the sponsors/monitors
  • Logging all required info in accountability logs*
  • Receiving shipments and stocking IP*
  • Managing extended expirations and drug recalls*
  • Randomization management*
  • IWRS and IVRS Submission*
  • Communication with drug sponsor and data coordinators throughout the study*
  • Close out visit
  • Budget and Billing

(*) Also applies to maintenance fee

Investigational Maintenance Fee

This fee may be paid to the Investigational Pharmacy either on a monthly or annual basis:

Monthly: $128.25

Annually: $1,539 (Inclusive of IDC)

Industry-Sponsored (initiated and funded by industry)

Investigator-Initiated and Funded by a Federally Supported Research Center (e.g. CTSC)


Funded by a Private Foundation or Federal Grant Investigator-Initiated and Industry-Funded


This fee is assessed monthly starting when inventory has been received until study close-out and study drug(s) are destroyed or returned to sponsor. This fee may also be paid on an annual basis

Please refer to the above table for task descriptions (*).


Subject Compensation and Reimbursement (ClinCard)
To implement ClinCard on your research projects please see the Researcher's Toolbox Training and Education Tools and Templates for more information. For questions please e-mail

Fee Type

Fee Amount

Fee Required


$4 per card

Pharma/Biotech/Device for all other projects please contact  


$1.25 per card load


Researcher's Toolbox

Contact Information

Joint Clinical Trials Office Weill Cornell Medicine /
1300 York Avenue,
Box 305
New York, NY 10065 Phone: (646) 962-8215 Fax: (646) 962-0536

Abbreviation Library