The CLIA Certificate of Waiver, Start to Finish

A CLIA Certificate of Waiver is the federal certificate a site needs before it runs even one waived test on a patient. Rapid strep, influenza and COVID-19 antigen tests, urine pregnancy tests, fingerstick glucose and A1c on a waived analyzer all fall under it. The Form CMS-116 instructions put it in capital letters: "WAIVED TESTS ARE NOT EXEMPT FROM CLIA. FACILITIES PERFORMING ONLY THOSE TESTS CATEGORIZED AS WAIVED MUST APPLY FOR A CLIA CERTIFICATE OF WAIVER."

It is by far the most common CLIA certificate. CMS's September 2026 laboratory statistics count 233,448 labs holding a Certificate of Waiver, about 81.6 percent of the 285,940 labs registered outside the two exempt states. Of those, 84,829 are physician office labs. The rest are pharmacies, urgent care centers, schools, nursing facilities, home health agencies and many other kinds of sites.

Who needs a Certificate of Waiver?

Under 42 CFR 493.2, a laboratory is any facility that examines material from the human body "for the purpose of providing information for the diagnosis, prevention, or treatment of any disease or impairment of, or the assessment of the health of, human beings." The CMS-116 instructions add that "CLIA applies even if only one or a few basic tests are performed, and even if you are not charging for testing."

A few situations fall outside that definition:

• Collection only. "Facilities only collecting or preparing specimens (or both) or only serving as a mailing service and not performing testing are not considered laboratories" (42 CFR 493.2). A site that swabs patients and ships every specimen to a reference lab does not need its own certificate.
• Patient self-testing. CMS's home testing FAQ says a test authorized by FDA for home use "is not regulated under CLIA when that test is self-administered" according to its labeling. Once staff perform the test or interpret the result, "a CLIA certificate would be required," and CMS names schools, shelters and jails as examples. Our post on home tests, self-testing and CLIA walks through the edge cases.
• Forensic, some research and SAMHSA drug testing. 42 CFR 493.3(b) excludes forensic-only testing, research that does not report patient-specific results, and SAMHSA-certified drug testing done under SAMHSA rules.
• New York and Washington. CMS describes both as running their own approved laboratory programs, with New York's exemption only partial. Physician office labs in New York still file the CMS-116; most other New York sites and every Washington site follow a state process. See the New York and Washington pages.

Which tests can a waiver lab perform?

Only tests that FDA has categorized as waived, used exactly as the manufacturer's instructions say. A test qualifies for waiver under 42 CFR 493.15(b) if it is cleared by FDA for home use, uses a method "so simple and accurate as to render the likelihood of erroneous results negligible," or poses "no reasonable risk of harm to the patient if the test is performed incorrectly." Categorization is attached to a specific test system, so check the exact kit or analyzer in FDA's CLIA database before you buy it. Our post on how to tell whether a test is CLIA-waived shows how to search it.

Two rules catch new sites. First, a waiver lab must "follow manufacturers' instructions for performing the test" (493.15(e)(1)). Second, CMS's home testing FAQ says that when a kit is used off-label, "the test complexity defaults to high complexity." Changing the specimen type or skipping a step can move a waived test out of a waiver lab's reach. More in off-label use of waived tests.

How does the application move from form to certificate?

1. Confirm the menu and the state rules. List every analyte, test name and manufacturer, and check whether your state adds its own registration or license. CMS's application page warns that "some states may have additional licensing requirements," and labs in those states must meet both.
2. Complete the CMS-116. A waiver applicant completes Sections I through VI and IX through X. The facility address must be the physical testing location and "cannot be a Post Office box or Mail Stop." Our section-by-section CMS-116 walkthrough covers each field.
3. The owner or director signs. 42 CFR 493.35(c)(2) requires the application to be signed by an owner or an authorized representative of the laboratory who attests that it will be operated under CLIA. The form's signature line reads "SIGNATURE OF OWNER/DIRECTOR OF LABORATORY," next to a consent to inspection.
4. Send it to the State Agency. "Completed 116 applications must be sent to your local State Agency. Do not send any payment with your completed 116 application." Find yours in CLIA State Agencies.
5. Pay from the emailed coupon. CMS's Quick Start Guide (March 2026) says you will receive a fee coupon by email with your laboratory's 10-character CLIA number and the total due. Payment goes through pay.gov by bank account, debit or credit card and is processed overnight.
6. Receive the certificate. The certificate arrives by email and can be viewed and reprinted online. CMS's application page says you can begin testing once you receive it. See when you may start testing.

Since March 1, 2026, CMS sends all fee coupons and certificates by email, so the email address on the CMS-116 matters more than it used to. CMS recommends "a business email address that many laboratory staff access and use." Details in email-only fee coupons and certificates.

How much does CMS charge for a Certificate of Waiver?

As of October 2026, the current CMS fee for a Certificate of Waiver is $248 for the two-year certificate, according to the fee schedule CMS links from its application page and the Minnesota Department of Health's CLIA fee table. A revised certificate (for example, a new director or address printed on it) costs $95, and a replacement copy costs $75. The lab pays these to CMS directly on pay.gov. The amounts change by notice in the Federal Register (42 CFR 493.638(b)), so read the figure on your own coupon. Our post on CLIA fees in 2026 explains why older tables showing $180 are out of date.

Does a waiver lab need a laboratory director?

Yes, but federal law sets no qualifications for one. CMS's application page says a lab with a Certificate of Waiver "must have a laboratory director. There are no federal education or experience qualifications required for the laboratory director." The CMS-116 asks for the director's name and credentials, and Section X asks which other labs that person directs. Some states set their own director rules, so check the state requirements index. The picture changes completely for PPM and nonwaived labs; see laboratory director requirements by certificate type.

What rules apply once the certificate is issued?

• Stay inside the certificate. A waiver lab must notify the State Agency before performing and reporting any test that is not waived (42 CFR 493.39(a)). Performing tests outside the certificate is a ground for suspension, limitation or revocation (493.1840(a)(2)).
• Report changes within 30 days. Ownership, name, location and director changes go to the State Agency within 30 days (493.39(b)). See changing your laboratory director and moving, renaming or selling a lab.
• Allow inspections. Waiver labs are not routinely surveyed, but CMS or its agent may inspect "at any time during the laboratory's hours of operation" to check a complaint, a risk to public health, or testing beyond the certificate (493.1775). More in when a waiver lab gets inspected.
• Expect enforcement to apply. Since January 27, 2024, CMS may impose alternative sanctions, including civil money penalties, on waiver labs (CMS-3326-F). See CLIA sanctions.
• Renew every two years. A Certificate of Waiver is "valid for no more than 2 years" (493.37(e)(1)). CMS's Quick Start Guide says waiver labs "will receive a renewal invoice 6 months before their certificate expires." See renewing a CLIA certificate.

CDC's waived testing page adds a practical warning: waived tests "are not completely error-proof," and errors happen when instructions are not followed or staff are unfamiliar with the test system. CDC's free Ready? Set? Test! booklet and self-assessment checklist are written for exactly these sites. Our post on what belongs in a waiver lab's compliance binder builds on them.

Is one certificate enough for several locations?

Usually not. A waiver lab "must file a separate application for each laboratory location" (42 CFR 493.35(a)). The rule has three exceptions: mobile or temporary testing sites covered under a home base, not-for-profit or government labs doing limited public health testing, and hospital labs on one campus under common direction (493.35(b)). A for-profit group of clinics or pharmacies does not fit any of them, so each fixed site needs its own certificate and pays its own fee. See one certificate per site, and the three exceptions.

How can White Glove CLIA help with a waiver application?

We prepare the CMS-116 and the test menu from each kit's instructions, check the state add-ons for your location, and hand the finished application to the owner or director to review and sign. Once it is signed, we can send it to the State Agency for you. The lab pays CMS on pay.gov from its own emailed coupon, and pays any state fee directly; we never collect or pass along a government fee, and our email never goes on your CMS-116. A Certificate of Waiver Application is $399 per site, or $549 per site with a compliance binder. Groups opening several sites can use the Multi-Site Waiver Package at $1,599 for five sites. The Certificate of Waiver hub has the full overview.