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CLIA application guide for U.S. clinics

Form CMS-116 explained: how to complete the CLIA Certificate of Waiver application (2026)

Start with your exact test menu, testing location and laboratory director. This guide explains the federal form and the steps from a signed application to a Certificate of Waiver.

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Educational preparation guidance, not legal or medical advice. This page does not confirm eligibility, approval, device-specific waived status or permission to test. Verify requirements with CMS, FDA and your state agency.

What is CMS-116, and which certificate does your clinic need?

Form CMS-116 is the CLIA Application for Certification. A clinic that tests human specimens for diagnosis, prevention, treatment or health assessment can be a laboratory under CLIA even when testing is a small part of its work. The application describes that laboratory; the certificate determines its permitted testing scope.

  • Certificate of Waiver: for testing categorized as waived. It does not authorize PPM, moderate-complexity or high-complexity testing.
  • Certificate for Provider Performed Microscopy Procedures (PPM): covers the specified PPM procedures and waived tests.
  • Certificate of Compliance or Certificate of Accreditation: routes for non-waived testing, with the applicable survey or accreditation and personnel requirements.

Choose the certificate for the highest complexity actually performed. A waived test is a specific test system used according to its manufacturer’s instructions; the name of the analyte alone is not enough.

Sources: CMS: Form CMS-116 (04/2026), including instructions · CMS: Apply for a CLIA Certificate · FDA: CLIA test-system database · eCFR: 42 CFR 493.15, laboratories performing waived tests

How to complete CMS-116, section by section

The headings below match the official downloadable Form CMS-116 (04/2026), opened November 9, 2026. Its printed OMB expiration is April 30, 2029. For a Certificate of Waiver, complete Sections 1–6 and 9–10, plus the signature block.

Sources: CMS: Form CMS-116 (04/2026), including instructions

Open the official CMS-116 PDFSee a fictional preparation packet

I. GENERAL INFORMATION

For a first application, check Initial application, enter the anticipated start date and leave the CLIA identification number blank; it is assigned during processing. Enter the facility name, federal tax identification number, the primary email plus the optional second and third emails and the fee-coupon email, then the facility phone and fax. The physical testing address must include the actual location and cannot be a P.O. box. Enter the laboratory director’s name and phone and the owner’s name and phone. The anticipated start date is not permission to begin testing.

Sources: CMS: Form CMS-116 (04/2026), including instructions · CMS: Apply for a CLIA Certificate · CMS: FAQs about the Transition to Paperless

II. TYPE OF CERTIFICATE REQUESTED

Check one certificate type. For a laboratory performing only waived tests, select Certificate of Waiver. The form directs waiver applicants to complete Sections I–VI and IX–X. PPM, compliance and accreditation applications follow different section requirements. Choose from the actual test menu and complexity, rather than from the clinic’s business name.

Sources: CMS: Form CMS-116 (04/2026), including instructions · CMS: Apply for a CLIA Certificate

III. TYPE OF LABORATORY

Select the single description that best fits the testing facility. The form includes Physician Office, Community Clinic, Pharmacy, Mobile Laboratory and other categories. Answer whether the laboratory is inside a CMS-certified health care facility and, when yes, list its CMS Certification Number(s). Do not assume every clinic or wellness business is a physician office; use the actual facility and operating arrangement.

Sources: CMS: Form CMS-116 (04/2026), including instructions

IV. HOURS OF LABORATORY TESTING

List the times when laboratory testing is actually performed for each day, using the form’s HH:MM format. These may differ from reception or business hours. Use the 24/7 checkbox only for continuous testing. For multiple sites, attach the additional hours in the same format.

Sources: CMS: Form CMS-116 (04/2026), including instructions

V. MULTIPLE SITES

Answer whether one certificate is requested for multiple testing locations. The general rule is a separate application for each laboratory location. Exceptions cover qualifying mobile or temporary operations, certain limited public-health testing by nonprofit or government laboratories, and qualifying hospital laboratories in contiguous campus buildings under common direction. Common ownership alone is not listed among those exceptions. If an exception applies, complete the relevant questions and site attachments; the form also requests vehicle identification numbers for mobile units. Confirm applicability with the state agency.

Sources: CMS: Form CMS-116 (04/2026), including instructions · eCFR: 42 CFR 493.35, application for a certificate of waiver

VI. WAIVED TESTING

List every waived analyte/test, test name and manufacturer in the 13-row table, identifying each test system or device used. Verify the exact kit or instrument/assay combination, specimen and intended use against FDA categorization and current manufacturer instructions. A generic name such as glucose or strep does not establish waived status. Enter the estimated total annual volume for all waived tests; attach more rows in the same format if needed. Count tests using the form’s counting instructions, rather than counting patient visits; quality-control, quality-assurance and proficiency-testing assays are excluded. Waiver-only applicants skip Sections VII and VIII.

Sources: CMS: Form CMS-116 (04/2026), including instructions · FDA: CLIA test-system database · FDA: CLIA Categorizations · eCFR: 42 CFR 493.15, laboratories performing waived tests

VII. PPM TESTING

This section lists provider-performed microscopy procedures and their estimated annual volume. Skip it for a waiver-only application. If the planned menu includes PPM, resolve the certificate type before filing; a Certificate of Waiver does not cover PPM testing.

Sources: CMS: Form CMS-116 (04/2026), including instructions

VIII. NON-WAIVED TESTING

The heading includes PPM testing for compliance or accreditation applicants. This section records non-waived systems, complexity and specialty/subspecialty volumes for those certificate types. It is not completed for a waiver-only application. If any planned testing is non-waived, reassess the application route instead of placing it in Section VI.

Sources: CMS: Form CMS-116 (04/2026), including instructions

IX. TYPE OF CONTROL

Select the ownership/control category that best describes the facility: voluntary nonprofit, for profit or government, using the listed choices. Answer the question about partial or full ownership or control by a non-U.S.-based government or entity and provide the country of origin if applicable. Reconcile the answer with the legal owner’s records and any required state supplement.

Sources: CMS: Form CMS-116 (04/2026), including instructions · CMS: Apply for a CLIA Certificate

X. DIRECTOR AFFILIATION WITH OTHER LABORATORIES

If this director also directs separately certified laboratories, list their CLIA numbers and laboratory names. The instructions include other Certificate of Waiver facilities. This is a director-affiliation question, separate from the multiple-site exception in Section V.

Sources: CMS: Form CMS-116 (04/2026), including instructions

Who signs the application?

The unnumbered signature block on page 7 asks for the printed name of the laboratory director/owner, then the signature of the laboratory director/owner and the date. It permits an ink signature or a secure electronic signature. Read the consent before signing: it concerns operation under applicable standards and access for authorized inspections. The block also carries the form’s warning that knowingly providing false or misleading information can be a criminal act punishable under federal law.

Under 42 CFR 493.35(c)(2), the waiver application must be signed by an owner or authorized laboratory representative. Confirm that the proposed owner/director signer has authority and that the state accepts the chosen signature method. WaivedLab prepares documents; the applicant reviews and signs. Any WaivedLab transmission requires separate written authorization.

Sources: CMS: Form CMS-116 (04/2026), including instructions · eCFR: 42 CFR 493.35, application for a certificate of waiver

Where do you submit CMS-116?

For the standard federal route, send the signed application and required documents to the CLIA state agency for the state where the laboratory is located. Do not mail it to CMS headquarters or to the paperwork-burden address printed on the form. Confirm the receiving office, submission channel, state supplements and signature rules before sending. State-specific or exempt-state programs can use a different route: Washington and New York run their own CMS-exempt programs, so follow those state guides instead of assuming the federal route.

Sources: CMS: Apply for a CLIA Certificate · CMS: Form CMS-116 (04/2026), including instructions · CMS: CLIA State Agency Contacts

Browse all state filing guides →

For examples of state instructions and their source-check dates, open a guide below. Follow that guide’s current findings and questions for the actual facility.

What is the federal waiver fee, and how do you pay in 2026?

The CMS fee schedule lists a $248 biennial federal Certificate of Waiver fee, meaning every two years. This is a government fee paid to CMS. Check the actual CMS notification and any separate state requirements; the federal amount is not a universal total for every jurisdiction.

Sources: CMS: CLIA Certificate Fee Schedule, effective January 27, 2024 · CMS: Apply for a CLIA Certificate

Do not send money with CMS-116. After processing, CMS emails the fee notification with the CLIA number. Since March 1, 2026, federal CLIA fee coupons and certificates are electronic, payments must go through Pay.gov and paper checks are no longer accepted. Keep a monitored business email on file.

  1. Wait for the fee notification and confirm the laboratory details and amount.
  2. Go to Pay.gov, search for CLIA and enter the CLIA ID from the invoice.
  3. Pay using an accepted bank account (ACH), debit card or credit card, and retain the receipt.

CMS says this federal paperless transition does not apply to CLIA-exempt state programs. Confirm their payment instructions with the relevant agency.

Sources: CMS: Form CMS-116 (04/2026), including instructions · CMS: FAQs about the Transition to Paperless

What happens after submission, and when can testing start?

The state agency processes the application. The emailed fee notification includes the laboratory’s unique ten-character alphanumeric CLIA number. After CMS receives payment, it sends the electronic certificate. CMS says you may begin testing once you receive the certificate; also confirm applicable state authorization and stay within the approved testing scope.

A CLIA number, an application delivery receipt or a paid invoice alone is not the certificate. If the notice or certificate does not arrive, check spam and contact the state agency. This guide does not promise an initial processing or approval date.

Sources: CMS: Apply for a CLIA Certificate · CMS: FAQs about the Transition to Paperless · CMS: Form CMS-116 (04/2026), including instructions

Where CLIA waiver applications go wrong

Frequently asked questions about CMS-116

What is the purpose of the CMS 116 form?

CMS-116 is the CLIA Application for Certification. It tells the agency about the laboratory, director, ownership, locations and testing so the laboratory can request the appropriate CLIA certificate. It is used for a Certificate of Waiver and other certificate types; submitting it does not itself authorize testing.

Sources: CMS: Form CMS-116 (04/2026), including instructions · CMS: Apply for a CLIA Certificate

How do I get my CLIA certificate?

For the standard federal route, complete CMS-116 and required supporting documents, send them to the CLIA state agency for your laboratory’s location, receive the emailed fee notification, pay through Pay.gov and receive the electronic certificate. Confirm additional state requirements before testing.

Sources: CMS: Apply for a CLIA Certificate · CMS: FAQs about the Transition to Paperless

What is a CLIA number?

It is the laboratory’s unique ten-character alphanumeric CLIA identification number. Leave the number field blank on an initial CMS-116 application. CMS says the fee notification includes the assigned number. A number on an invoice is not the certificate or permission to start testing.

Sources: CMS: Form CMS-116 (04/2026), including instructions · CMS: Apply for a CLIA Certificate

How do I get a CLIA waiver certificate?

First confirm that every planned test system is waived for the intended use. On CMS-116, select Certificate of Waiver, complete Sections I–VI and IX–X, sign and submit through the confirmed state agency route with required state documents. Pay the federal fee after the notification arrives, then receive the certificate and satisfy applicable state requirements before testing.

Sources: CMS: Form CMS-116 (04/2026), including instructions · FDA: CLIA test-system database · CMS: Apply for a CLIA Certificate

Who signs CMS-116?

The form’s signature line is for the laboratory owner/director, with a date and either an ink or secure electronic signature. The waiver application regulation requires an owner or authorized laboratory representative to sign. Confirm the signer’s authority and the state’s accepted signature method before submission. WaivedLab prepares the packet; it does not sign for the applicant.

Sources: CMS: Form CMS-116 (04/2026), including instructions · eCFR: 42 CFR 493.35, application for a certificate of waiver

Can I start testing while my application is pending?

For a new Certificate of Waiver, CMS says testing can begin once you receive the CLIA certificate after payment. An application, anticipated start date, CLIA number or payment receipt alone is not that certificate. Confirm any additional state authorization and use only tests within the certificate’s scope.

Sources: CMS: Apply for a CLIA Certificate · CMS: Form CMS-116 (04/2026), including instructions

Turn the form into your clinic’s preparation checklist

Use the checker to organize your test menu, then read your state’s filing guide and compare the fictional sample packet. Keep signatures, tax identifiers and private documents out of public inquiries.

Run the checker State filing guidesFictional sample packet

Sources checked 2026-11-09

Official CMS and FDA materials and the cited eCFR provisions were consulted for this guide. Recheck the application edition and state instructions before filing.