A CLIA Certificate of Waiver is the federal authorization that lets a clinic, treatment program, or testing site legally perform simple, low risk lab tests, including most instant drug test cups, on human specimens. You apply using Form CMS-116, submit it to your state's CLIA agency, pay a biennial fee, and renew every two years. This guide walks through what CLIA actually is, who needs a waiver, how the CMS-116 process works, and what CLIA-waived status means when you are choosing test cups for your program.
What CLIA Is
CLIA stands for the Clinical Laboratory Improvement Amendments, the federal law Congress passed in 1988 to set standards for laboratory testing performed on human specimens, regardless of where or by whom the test is performed. The Centers for Medicare and Medicaid Services (CMS) administers the CLIA program, and the requirements are based on the complexity of the test rather than the type of facility running it. That is why a hospital lab, a small occupational health clinic, and a rehabilitation program can all fall under the same set of rules once they perform tests on patient specimens.
CMS defines a laboratory broadly under CLIA: any facility that performs even one test on "materials derived 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" is considered a laboratory, and this includes tests categorized as waived. If your clinic performs even a single waived drug screen for diagnostic, treatment, or health assessment purposes, CLIA applies to you.
What a Waived Test Is
Under 42 CFR 493.15, waived tests are simple laboratory examinations and procedures that meet one of three criteria: they are cleared by the FDA for home use, they use methodologies so simple and accurate that the chance of an erroneous result is negligible, or they pose no reasonable risk of harm to the patient if performed incorrectly. The FDA, not CMS, determines which specific test systems meet this standard. A manufacturer submits evidence to the FDA, and if the agency agrees the test qualifies, that specific device is added to the FDA's list of CLIA-waived tests. This is also why waived status is tied to a specific product, not a category of test in general. Before you rely on a device for waived-scope testing, confirm the exact model appears in the FDA's public CLIA database rather than assuming any cup or dip card qualifies.
Waived vs. Moderate vs. High Complexity
The FDA sorts every cleared test system into one of three complexity tiers. For tests that are not automatically waived, the FDA scores the test against seven criteria on a "scorecard," covering knowledge required, training, reagent handling, operational steps, calibration and quality control, troubleshooting, and interpretation. Each criterion is scored 1, 2, or 3, and the total determines the category.
| Complexity | How it is determined | Certificate required | Routine CMS or state survey |
|---|---|---|---|
| Waived | Meets 42 CFR 493.15(c) criteria, or cleared/approved by FDA for home use | Certificate of Waiver | Not subject to routine surveys; complaint driven inspections only |
| Moderate | FDA scorecard total of 12 or less across the seven criteria | Certificate of Compliance or Certificate of Accreditation (Certificate of Registration while pending initial survey) | Subject to biennial survey by CMS, a state agency, or an approved accreditor |
| High | FDA scorecard total above 12; systems not yet categorized default to high complexity | Certificate of Compliance or Certificate of Accreditation, plus qualified technical and laboratory director credentials | Subject to biennial survey by CMS, a state agency, or an approved accreditor |
Most instant drug test cups, dip cards, and oral fluid screens that clinics buy in volume have gone through the FDA's CLIA Waiver by Application process and are marketed specifically as CLIA-waived, which is what makes a Certificate of Waiver the right certificate type for a typical clinic testing program rather than a Certificate of Compliance.
Do You Actually Need One?
Not every testing setup needs CLIA certification. CMS lists specific exceptions, including laboratories that only perform testing for forensic purposes, research laboratories that do not report patient-specific results, and laboratories certified by SAMHSA for drug testing that meets SAMHSA's own guidelines. CMS also notes that drug testing performed strictly for employment purposes generally does not require a CLIA certificate, unless the same clinic offers or makes available individual treatment in connection with that testing, in which case a certificate is required. Clinics, treatment programs, occupational health centers, and any facility that reports results back for clinical, diagnostic, or treatment purposes should assume they need a Certificate of Waiver if they are only running waived tests.
How to Apply: The CMS-116 Process
The application itself is a single federal form.
- Complete Form CMS-116. This is the CLIA Application for Certification, available as a PDF from CMS. It asks for your facility information, the tests you plan to perform, and your laboratory director's information.
- Submit it to your state agency, not CMS directly. CMS routes CLIA applications through each state's designated CLIA agency, which processes the paperwork and communicates back with your facility. New York and Washington run their own approved laboratory programs and have separate contact points, so confirm with your state agency if you are located in either state.
- Name a laboratory director. A Certificate of Waiver requires a laboratory director, but CMS is explicit that there are no federal CLIA educational or experience requirements for that role at the waiver level, unlike moderate and high complexity certificates.
- Wait for your fee coupon. Once your state agency processes the application, you will receive a fee remittance coupon showing the amount due and your new CLIA identification number, a ten-character code that identifies your lab for the life of the certificate.
- Pay the fee and receive your certificate. You generally may begin waived testing once you have received your certificate, though some states layer on additional licensing requirements, so confirm with your state agency before you start testing patients.
What It Costs
CLIA certificate fees are set by CMS, not chosen by individual clinics, and the amount is published biennially by CMS with adjustments announced through Federal Register notice. According to CMS's published CLIA Certificate Fee Schedule, the biennial fee for a Certificate of Waiver is a flat amount that does not vary by test volume or number of specialties, unlike the fee schedules for compliance and accreditation certificates, which scale with annual test volume. Because CMS updates this schedule periodically, confirm the current fee directly against CMS's fee schedule page before budgeting, rather than relying on a number quoted secondhand. Your state agency can also confirm the exact amount due once your application is processed, since a small number of states charge additional state licensing fees on top of the federal CLIA fee.
Renewal Every Two Years
A Certificate of Waiver is valid for no more than two years from the date it is issued. To renew, you complete the renewal application CMS prescribes and return it to your state agency not less than nine months and not more than one year before your current certificate expires. Miss that window and you risk a lapse in your ability to legally perform even simple waived testing, which is a real operational risk for a clinic or treatment program that depends on same-day results. Mark your certificate's expiration date and build the renewal window into your compliance calendar the same way you would track any other regulatory deadline.
Choosing CLIA-Waived Test Cups for Your Program
Once you hold a Certificate of Waiver, your testing menu is legally limited to tests categorized as waived. That makes the CLIA-waived designation on a product's packaging and instructions for use a purchasing requirement, not a marketing detail. When you are sourcing CLIA-waived and FDA-cleared drug test cups, confirm the specific device is listed in the FDA's CLIA database before you build a testing program around it, since waiver status attaches to the exact test system, not to drug test cups as a category. ASC's CLIA-waived drug test supplies are built around this requirement, which is part of why they are a common fit for hospital and clinic drug testing programs, medical center testing kits, and drug and alcohol testing solutions for rehabilitation and treatment centers, where a Certificate of Waiver is typically the certificate on file. If your program also collects oral fluid specimens, the same waived-status rule applies to CLIA-waived oral fluid tests, so verify the specific device before adding it to your menu.
If your clinic later wants to add a test that is not on your waiver's test list, whether a different analyte or a more complex confirmation method, federal rules require you to meet the requirements for a Certificate of Compliance or Certificate of Accreditation before performing it, and to reapply using the same CMS-116 form. You cannot simply start running a non-waived test under an existing Certificate of Waiver.
Frequently Asked Questions
Does a clinic doing employment drug testing need a CLIA Certificate of Waiver?
Generally no, if the testing is done strictly for employment purposes. CMS states that a CLIA certificate is not required for drug testing done for purposes of employment, unless the same facility also offers or makes available individual treatment, in which case a CLIA certificate is required.
How long does it take to get a CLIA Certificate of Waiver?
CMS does not publish a fixed processing timeline. After you submit Form CMS-116 to your state agency, the agency processes the application and issues a fee remittance coupon. Once you pay the fee, your certificate is mailed to you, and you generally may begin testing once you have received it, though some states add their own steps.
Who can serve as the laboratory director for a Certificate of Waiver?
A laboratory with a CLIA Certificate of Waiver must have a laboratory director, but there are no federal CLIA educational or experiential qualifications for that role, unlike the requirements for moderate and high complexity testing directors.
What happens if I want to add a test that is not covered by my waiver?
A laboratory with a Certificate of Waiver that wishes to perform tests not listed in the waived test category must meet the requirements for a Certificate of Compliance or Certificate of Accreditation, as applicable, and must reapply using the CMS-116 form used for the original certification.
Related reading
This article is for general informational purposes only and does not constitute legal, regulatory, or medical advice. CLIA requirements, fees, and forms are set by CMS and can change, and individual states may impose additional licensing requirements on top of federal CLIA rules. Verify current requirements, forms, and fees directly with CMS and your state CLIA agency before applying for or relying on a Certificate of Waiver.
