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National Institutes of Health (NIH)

Maximizing and protecting grant funding requires specialized knowledge. Cherry Bekaert federal grant advisors help you navigate FAR Part 31 and NIH Supplemental Regulation requirements and reduce audit risk.

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NIH Grants Compliance and Audit Readiness To Reduce Risk

For organizations receiving National Institutes of Health (NIH) funding, or funding from its parent, the Department of Health and Human Services (HHS), effective grant management is just as important as the research itself. NIH awards carry complex administrative and financial requirements that demand careful oversight throughout the life of the grant to help support compliance, accountability, and long-term funding success.

All of these funding awards are “cost reimbursable” type funding vehicles, which require the recipient to properly account for all actual project-specific costs in accordance with the Federal Acquisition Regulation (FAR) Part 31 and NIH Supplemental Regulations. All NIH funding awards are subject to several types of audits, and the risk of noncompliance includes financial penalties, project suspension or debarment from federal funding.

For decades, Cherry Bekaert’s federal grants advisors have helped clients across the country procure, manage and survive audits of NIH federal funding awards. Our advisors know the agencies and regulations — and we know how to help our clients avoid common compliance pitfalls.

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Need help maintaining your accounting system in accordance with 2 CFR Part 200 and the NIH Grants Policy Statement? Our advisors help you stay compliant and audit ready. 

NIH Grants Policy Statement 

The NIH Grants Policy Statement outlines the terms and conditions that come with accepting a NIH grant, which are almost always cost-reimbursable-type funding awards. If you have accepted a NIH Grant, you are subject to the following accounting requirements: 

Form SF-425, Federal Financial Report (FFR)

Filed within 30 days after each annual budget period and within 120 days after the end of the grant, this report reconciles the funds drawn from the Payment Management System (PMS) to the actual spending from the company’s accounting system. The form sign-off includes a certification (on line 13) that “any false, fictitious, or fraudulent information may subject me to criminal, civil, or administrative penalties”.

Improper cash draws from the PMS and improper supervision/ accountability of subcontractors and consultants are the most common audit findings that require repatriation of funds.

2 CFR 200, Subpart F – The Uniform Guidance Audit

If an awardee has annual expenditures from covered grants that exceeds $1M, then it is also subject to an annual Uniform Guidance Audit (UGA). The awardee is required to hire and pay for a CPA firm professionally qualified to conduct this type of audit, which encompasses both financial and compliance components within nine months of the company’s fiscal year-end. The auditor’s report is reviewed by the Office of the Inspector General (IG) for quality control purposes, and the CPA firm’s work papers may be audited by the IG.

The annual negotiation of your incurred cost submission will not occur until the Division of Financial Advisory Services (DFAS) is provided a copy of your final Uniform Guidance Audit report.

Negotiating a Fringe and F&A Rate

Unless you have elected to use the de minimis indirect cost rate or the SBIR safe rate, you are required to prepare an annual incurred cost submission within 180 days after your company’s fiscal year end that reflects all general ledger expenses on a generally accepted accounting principles (GAAP) basis. This report is used to settle the final accounting for all HHS/NIH grants and contracts, including the negotiation of an indirect cost rate agreement or Negotiated Indirect Cost Rate Agreement (NICRA).

To receive a NICRA, the following must be filed:

  • A copy of your financial statements prepared in accordance with GAAP.
  • All expenses must be accounted for and reported as either direct, indirect and unallowable based on FAR Part 31 and the NIH Supplemental Regulations.
  • All labor costs must be distributed through the general ledger on an accrual basis and must reconcile with the quarterly payroll tax returns – a cash-basis document.
  • Indirect costs need to be proportionally allocated to all grant and non-grant activities based on the methodology used in your NICRA.
  • A schedule detailing all employee salaries costs distributed, as well as an organization chart.
  • An accounting policies and procedures manual and any employee handbooks.
  • Detailed descriptions of all consulting and subcontracting costs.
  • All the fringe and F&A rate-supporting calculations for the year.

Once the annual incurred cost submission is filed, any over-billing or under-billing of indirect expenses must be proactively remedied on a grant-by-grant basis.

Form SF-425, Federal Financial Report (FFR)

Filed within 30 days after each annual budget period and within 120 days after the end of the grant, this report reconciles the funds drawn from the Payment Management System (PMS) to the actual spending from the company’s accounting system. The form sign-off includes a certification (on line 13) that “any false, fictitious, or fraudulent information may subject me to criminal, civil, or administrative penalties”.

Improper cash draws from the PMS and improper supervision/ accountability of subcontractors and consultants are the most common audit findings that require repatriation of funds.

2 CFR 200, Subpart F – The Uniform Guidance Audit

If an awardee has annual expenditures from covered grants that exceeds $1M, then it is also subject to an annual Uniform Guidance Audit (UGA). The awardee is required to hire and pay for a CPA firm professionally qualified to conduct this type of audit, which encompasses both financial and compliance components within nine months of the company’s fiscal year-end. The auditor’s report is reviewed by the Office of the Inspector General (IG) for quality control purposes, and the CPA firm’s work papers may be audited by the IG.

The annual negotiation of your incurred cost submission will not occur until the Division of Financial Advisory Services (DFAS) is provided a copy of your final Uniform Guidance Audit report.

Negotiating a Fringe and F&A Rate

Unless you have elected to use the de minimis indirect cost rate or the SBIR safe rate, you are required to prepare an annual incurred cost submission within 180 days after your company’s fiscal year end that reflects all general ledger expenses on a generally accepted accounting principles (GAAP) basis. This report is used to settle the final accounting for all HHS/NIH grants and contracts, including the negotiation of an indirect cost rate agreement or Negotiated Indirect Cost Rate Agreement (NICRA).

To receive a NICRA, the following must be filed:

  • A copy of your financial statements prepared in accordance with GAAP.
  • All expenses must be accounted for and reported as either direct, indirect and unallowable based on FAR Part 31 and the NIH Supplemental Regulations.
  • All labor costs must be distributed through the general ledger on an accrual basis and must reconcile with the quarterly payroll tax returns – a cash-basis document.
  • Indirect costs need to be proportionally allocated to all grant and non-grant activities based on the methodology used in your NICRA.
  • A schedule detailing all employee salaries costs distributed, as well as an organization chart.
  • An accounting policies and procedures manual and any employee handbooks.
  • Detailed descriptions of all consulting and subcontracting costs.
  • All the fringe and F&A rate-supporting calculations for the year.

Once the annual incurred cost submission is filed, any over-billing or under-billing of indirect expenses must be proactively remedied on a grant-by-grant basis.

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Gain experienced guidance to help your company maintain compliance, strengthen audit readiness and manage NIH reporting requirements.

Benefits of Using Cherry Bekaert for Your NIH Grant Needs

NIH funding brings complex compliance requirements. Backed by an experienced team with specialized knowledge of NIH grant accounting and compliance requirements, Cherry Bekaert helps you maintain compliant accounting practices, strengthen audit readiness, and manage NIH reporting obligations so you can focus on your research objectives.

“Cherry Bekaert combines specialized NIH compliance knowledge with accounting and advisory support to help grant recipients confidently navigate the complexities of federal funding. By taking the time to understand your company's unique goals and requirements, we deliver tailored solutions that support compliance, strengthen audit readiness, and enable you to focus on driving sustainable growth and maximizing the value of your NIH funding.” 
Ed Jameson
Government Contracting Leader

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NIH Consulting FAQs

NIH grants are subject to the NIH Grants Policy Statement and require compliance with SF-425 reporting, Uniform Guidance requirements, and other accounting, reporting and audit obligations applicable to NIH funding recipients. 

The NIH Grants Policy Statement outlines the terms and conditions associated with accepting and managing NIH grant funding. NIH grants are generally cost-reimbursable funding awards that require recipients to properly account for project-specific costs and comply with applicable regulations. 

SF-425, also known as the Federal Financial Report (FFR), is used to reconcile funds drawn from the Payment Management System (PMS) with actual spending recorded in the organization's accounting system. NIH grant recipients are required to submit these reports as part of their grant compliance responsibilities. 

A Uniform Guidance Audit (UGA) is a compliance audit conducted under government auditing standards to evaluate whether an organization has complied with the terms and conditions of its federal awards. The audit includes both financial and compliance components. 

Organizations that exceed the $1 million federal expenditure threshold during their fiscal year are required to undergo a Uniform Guidance Audit.  

Common compliances challenges that can lead to audit findings if not properly managed include SF-425 reporting, improper management of funds drawn from the Payment Management System, poor accountability for subcontractors and consultants and failure to maintain compliance with grant-specific regulations. 

NIH funding awards may be subject to multiple types of audits. Maintaining compliant accounting records, accurate reporting, and adherence to NIH requirements can help grant recipients prepare for audit scrutiny and support ongoing compliance. 

Cherry Bekaert provides accounting, compliance, reporting and audit readiness support for organizations receiving NIH funding. Our team has extensive experience with NIH Grants Policy Statement compliance, SF-425 reporting requirements, Uniform Guidance Audits and representation during audits. 

NIH grants contain specialized accounting, reporting, and compliance requirements that differ from traditional commercial and other federal agency accounting. Recipients must properly account for project costs and comply with agency-specific regulations governing federal funding. 

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