If your organization receives a SAMHSA grant, the rules governing how you account for, manage, and audit that money have changed. The Substance Abuse and Mental Health Services Administration sits inside the U.S. Department of Health and Human Services (HHS), and HHS has moved its grants from the old 45 CFR Part 75 framework to the government-wide Uniform Guidance at 2 CFR Part 200. For behavioral health providers, community mental health centers, and substance use treatment organizations, a SAMHSA grant is no longer governed by a cosmetic citation swap. The shift reshapes cost principles, procurement standards, and the single audit you may owe.
Quick answer: Effective October 1, 2025, HHS fully adopted 2 CFR Part 200 (the Uniform Guidance) in place of 45 CFR Part 75 for its awards, including SAMHSA grants, with HHS-specific exceptions codified in 2 CFR Part 300. Your SAMHSA award now follows the same federal cost principles, administrative requirements, and audit rules as most other federal grants, and if you expend $1,000,000 or more in total federal awards in a fiscal year, you must obtain a single audit.
This article explains what actually changed, why the dollar thresholds matter, and the specific items your finance team and auditor should test before year end. The goal is practical: fewer findings, cleaner draws, and a defensible audit file. Each section ties back to a step you can take now, not after fieldwork begins.
What Changed: From 45 CFR Part 75 to 2 CFR 200
For years, HHS grantees followed 45 CFR Part 75, the department’s own implementation of the Uniform Guidance. The substance was similar to 2 CFR 200, but the citations, cross-references, and a handful of HHS-specific provisions lived in a separate part of the regulations. That created friction for organizations juggling awards from multiple federal agencies, because the same concept could carry two different citations depending on the funder.
HHS adopted the change in two phases. In a final rule published in the Federal Register on October 2, 2024 (89 FR 80055), HHS announced that it would rescind 45 CFR Part 75 and fully adopt 2 CFR Part 200, with the full transition taking effect October 1, 2025. As part of that move, HHS relocated twelve agency-specific provisions to a new part, 2 CFR Part 300. Part 300 carries the HHS-particular rules on topics such as special provisions for for-profit recipients, statutory and national policy requirements, and non-discrimination. The general framework now points to the government-wide text, which means a single rulebook covers most of your obligations.
For a SAMHSA grant, the practical effect is that your terms and conditions, your notice of award, and your auditor’s compliance testing all reference 2 CFR 200. If your internal policies, your indirect cost documentation, or your accounting manual still cite 45 CFR Part 75, those references are now stale and should be updated. Auditors increasingly expect to see policies aligned to the controlling regulation, and a policy library pointing at superseded rules is an easy finding to avoid.
This transition layered on top of the broader 2024 revision to 2 CFR Part 200, which the Office of Management and Budget finalized for projects starting on or after October 1, 2024. Organizations are therefore absorbing two related changes: the OMB-level content updates that took effect October 1, 2024, and the HHS-level framework migration that took full effect October 1, 2025. In fact, HHS applied several of the increased OMB thresholds, including the audit and de minimis changes, beginning October 1, 2024, ahead of its full Part 200 adoption a year later. Both feed directly into how a SAMHSA grant is audited, so treating them as one combined update keeps your policy review efficient. You can confirm the current government-wide text at the eCFR text of 2 CFR Part 200.
How the $1,000,000 Single Audit Threshold Affects a SAMHSA Grant
The headline number for most grantees is the single audit threshold. Under the 2024 revision to 2 CFR Part 200, the single audit threshold rose from $750,000 to $1,000,000. An organization must obtain a single audit, or a program-specific audit where eligible, only when it expends $1,000,000 or more in total federal awards during its fiscal year, applying to fiscal years beginning on or after October 1, 2024.
This is an expenditure test, not an award test. It looks at federal dollars expended across all federal programs combined, not the size of any single SAMHSA grant. A treatment provider with an $800,000 SAMHSA award, a $300,000 HRSA award, and modest pass-through federal funds can cross the $1,000,000 line in aggregate even though no individual grant approaches it. Tracking expenditures program by program throughout the year is the only reliable way to know where you land.
The revision also raised the Type A program threshold, which determines which programs receive deeper audit scrutiny. For entities with $34,000,000 or less in total federal expenditures, the Type A threshold is now $1,000,000, up from the prior $750,000 figure tied to the old $25,000,000 ceiling. Smaller behavioral health organizations that previously saw a SAMHSA grant flagged as a major program may find the major-program determination shifts under the new figures, though that depends on your full federal portfolio and the auditor’s risk assessment.
If you sit just below $1,000,000 in expenditures, do not assume you are permanently exempt. Multi-year SAMHSA grants, supplemental awards, and carryover balances can push next year’s expenditures over the line. Modeling your federal expenditures forward, and discussing the trajectory with your audit team early, prevents a last-minute scramble to engage a single audit you did not budget for. Our audit and assurance services team helps grantees forecast that threshold and scope the engagement before fieldwork begins.
Cost Principles and Indirect Rates Under the Uniform Guidance
Beyond the audit trigger, 2 CFR 200 governs which costs you can charge to a SAMHSA grant and how. The cost principles in Subpart E set the standards for allowability, allocability, and reasonableness, and they require documentation that connects each charge to the federal program that benefits from it. Salaries allocated across funding sources, for example, need support consistent with the standards for charges to federal awards, not just a budget estimate.
The 2024 revision raised the de minimis indirect cost rate from 10% to 15% of modified total direct costs. A recipient or subrecipient that does not have a current federally negotiated indirect cost rate may elect to charge up to 15% under the de minimis option, and may determine the appropriate rate up to that limit. For many behavioral health nonprofits that have never negotiated a formal rate, this is a meaningful increase in recoverable overhead, but it must be applied consistently and documented in your accounting policies. The federal summary of these changes is available through the EPA overview of the 2024 revision to 2 CFR Part 200.
Procurement is another area where the Uniform Guidance bites. The procurement standards in Subpart D require written procurement policies, documented competition, and conflict of interest safeguards. A common finding for first-time single audit clients is sole-source purchasing without the required justification, or missing documentation that vendors were evaluated competitively. Tightening these procedures before an auditor arrives costs far less than remediating a finding afterward.
Subrecipient monitoring also deserves attention. If your SAMHSA grant flows dollars to subrecipients, the subrecipient monitoring requirements in 2 CFR 200.331 through 200.333 require risk assessment, written subaward terms, and ongoing monitoring. Pass-through entities are accountable for what their subrecipients do with federal money, and weak monitoring is a recurring source of audit findings. Organizations operating in this space can find sector-specific guidance through our behavioral health practice, which works with providers on grant compliance and reporting.
How Should You Prepare Your SAMHSA Audit File?
Start with a clean schedule of expenditures of federal awards (SEFA). The SEFA drives the single audit, and errors here, such as misclassified programs or omitted pass-through funds, cascade into every other test. Reconcile your SEFA to your general ledger and to your federal drawdowns monthly rather than reconstructing it at year end.
Next, refresh your written policies so they cite 2 CFR 200 and, where relevant, 2 CFR 300, rather than 45 CFR Part 75. Confirm your indirect cost methodology, document any de minimis election at the 15% rate, and verify that your time-and-effort records support payroll charges to the SAMHSA grant. These three areas, allowability documentation, indirect rates, and labor allocation, generate a large share of grant findings, so they reward early attention.
Finally, assemble the compliance evidence your auditor will request: procurement files with competition documentation, subaward agreements and monitoring records, cash management records showing draws matched to needs, and your reporting submissions. Walking into fieldwork with this file organized shortens the engagement and reduces the odds of a finding that must be reported to the federal government. An organized file also gives your board and your funder confidence that federal dollars are controlled.
Frequently Asked Questions
When did SAMHSA grants become subject to 2 CFR 200?
HHS announced the change in a final rule published in the Federal Register on October 2, 2024, and fully adopted 2 CFR Part 200 in place of 45 CFR Part 75 effective October 1, 2025. That adoption applies to SAMHSA awards because SAMHSA is an HHS agency. Twelve HHS-specific provisions were relocated to 2 CFR Part 300. Review your current notice of award and terms and conditions to confirm which framework governs your specific grant period.
What is the single audit threshold for a SAMHSA grant?
The single audit threshold is $1,000,000 in total federal expenditures during your fiscal year, increased from $750,000 under the 2024 revision to 2 CFR Part 200, effective for fiscal years beginning on or after October 1, 2024. The test aggregates all federal awards you expend, not just your SAMHSA grant, so combined federal funding can trigger the requirement.
Did the indirect cost rate change under the Uniform Guidance?
Yes. The de minimis indirect cost rate rose from 10% to 15% of modified total direct costs under the 2024 revision. Recipients and subrecipients without a current federally negotiated rate may elect to charge up to 15%, provided the election is documented and applied consistently.
Do I need a single audit if my SAMHSA grant is under $1,000,000?
Not based on that grant alone, but the threshold looks at total federal expenditures across all your federal awards combined. If your SAMHSA grant plus other federal funding reaches $1,000,000 in a fiscal year, a single audit is required. Track expenditures by program throughout the year and project forward so a multi-year or supplemental award does not push you over the line unexpectedly.
