CLIA Fees in 2026, and Why the Old Fee Schedule Is Wrong

CLIA is funded entirely by the labs it regulates. The CMS-116 instructions say the law "requires financing of all regulatory costs through fees assessed to affected facilities," and 42 CFR 493.638 says the total of CLIA fees "must be sufficient to cover the general costs of administering the laboratory certification program." That is why the fees went up in 2024 and why they are built to keep moving.

All amounts below are the current CMS fees as of October 2026, taken from the CLIA Certificate Fee Schedule (updated 2024) that CMS links from its "Apply for a CLIA Certificate" page, and checked against the fee table published by the Minnesota Department of Health, a CLIA State Agency. The lab pays them to CMS from its own emailed coupon.

What does each certificate cost in 2026?

The schedules are defined in 42 CFR 493.638(c)(3) by annual test volume and number of specialties. Waived tests and tests run for quality control, quality assurance or proficiency testing do not count toward volume.

One caution on revised certificates for PPM and Accreditation labs: the CMS schedule and Minnesota's table do not agree on which of those two pays $95 and which pays $150. The amount on your coupon controls.

Which schedule does a nonwaived lab fall into?

Volume and specialties decide it, and both come from Section VIII of the CMS-116. The counting rules in the form's instructions are specific:

• For chemistry, "each non-calculated analyte is counted separately," so a lipid panel of total cholesterol, HDL, LDL and triglycerides "equals 4 tests."
• For hematology, each measured analyte of a complete blood count counts separately, and the white cell differential counts as one test.
• For urinalysis, a dipstick counts as one test "regardless of the number of reagent pads on the strip," and belongs with waived testing anyway.
• Calculations, quality control, quality assurance and proficiency testing are never counted.

Specialties follow 42 CFR 493.638(c)(2), which groups subspecialties under microbiology, serology, chemistry, hematology, immunohematology, pathology, radiobioassay, histocompatibility and clinical cytogenetics. A clinic running a few thousand chemistry and hematology tests a year in two specialties lands in Schedule A, with a $223 certificate fee. Overstating volume pushes a lab into a higher schedule; understating it is a misstatement on a signed federal form.

Why do older tables say $180?

Because they predate the 2023 fee rule. CMS-3326-F, published December 28, 2023 at 88 FR 89976, made the fee provisions effective January 27, 2024. CMS's summary memo for State Agencies (QSO-24-03-CLIA) lists what changed:

• an 18 percent across-the-board increase to existing fees "to stabilize the overall program";
• an extra $25 on the Certificate of Waiver fee "to offset program obligations to FDA for its role" in categorizing waived tests (the rule's preamble says this "will increase the current $180.00 biennial CoW fee to $205.00" before the percentage increases);
• a first biennial inflation adjustment of 4.9598 percent;
• new fees for revised and replacement certificates, follow-up surveys, substantiated complaint surveys and desk reviews of unsuccessful proficiency testing; and
• a standing rule to raise fees every two years.

The result is the $248 waiver fee in effect today. A fee schedule marked 2019 still circulates on cms.gov and in old binders; it is out of date and should not be used to budget.

How will CLIA fees change from here?

Under 42 CFR 493.680, fees are subject to a biennial two-part increase. First, CMS applies the compounded CPI-U inflation rate over two years if it is above zero. Second, if total fees still "do not match or exceed actual program obligations based on a review of the previous 2 years' obligations," CMS applies an additional across-the-board increase. Each increase is published "as a notice in the Federal Register," and the lab owes "the amount listed in the most recent notice… at the time the application, renewal, change in certificate type, or reinstatement is processed" (493.638(b)(3)). So a renewal coupon can show a different figure than the one you paid two years ago. Budget from the coupon, not from memory.

What else do nonwaived labs pay?

Compliance and Accreditation labs pay more than the certificate fee:

• Compliance survey fee. A Certificate of Compliance lab pays a biennial fee to cover the cost of determining compliance (493.643). The CMS schedule lists national averages from $446 for a low-volume lab to $5,459 for Schedule J, plus $411 for every additional 500,000 tests. The schedule says to contact your State Agency for the specific amount.
• Validation fee. A Certificate of Accreditation lab pays 5 percent of the equivalent survey cost every two years, "whether the accredited laboratory has a validation inspection or not" (493.645(a)(1)). The CMS schedule lists averages from $22 to $273. The accreditation organization's own fees are separate.
• Cost-based fees. Follow-up surveys after deficiencies, added-specialty surveys, substantiated complaint surveys and desk reviews of unsuccessful proficiency testing are billed at the State Agency hourly rate times the hours spent, including travel (CMS lists an average rate of $111.81 for fiscal year 2024). HHS "revokes the laboratory's certificate" for failure to pay these (493.643(d)).

Waiver and PPM labs pay no survey fee for routine inspections, because they do not get routine inspections (493.643(a)). They can still be billed for a substantiated complaint investigation (493.645(b)).

How are CLIA fees paid?

Online only. The CMS-116 says "Do not send any payment with your completed 116 application." After the State Agency processes it, CMS emails a fee coupon with the CLIA number and the amount due. CMS's CLIA page says labs "must pay their CLIA certification fee online though pay.gov" and that CMS "no longer accepts paper checks." The certificate is not issued until the fee is paid (493.655(a)). See email-only fee coupons since March 2026.

Where do state fees fit?

Separately. A state lab registration, license or permit has its own fee schedule, paid to the state, and the amounts vary widely. Check your state in the state requirements index and read state lab licensing on top of CLIA.

Do our service fees ever include government fees?

No. White Glove CLIA's prices are for preparing and tracking filings: $399 per site for a Certificate of Waiver Application, $599 per site for a PPM Certificate Application, $149 per change and $299 per year for Renewal and Compliance Tracking (see pricing). The lab pays CMS on pay.gov from its own coupon and pays the state directly. We never collect, forward or bill a government fee, and nothing we send is styled as a CMS bill. CMS warned labs in October 2026 about third-party mailings "styled as bills or invoices"; see look-alike CLIA invoices.