How to Get a CLIA Certificate

If you examine specimens from the human body to diagnose, prevent or treat disease, or to assess health, CLIA calls you a laboratory (§ 493.2), even if the lab is one counter in a clinic. You need one of five certificates, and the menu decides which. CMS: "the certificate a laboratory obtains must be for the most complex category of testing the laboratory performs."

Fees: CMS fee schedule, updated 2024, read 2026-10-23, paid every two years.

Nobody applies for a Certificate of Registration on its own. On Form CMS-116 you tick Compliance or Accreditation, and the form says "you will initially pay for and receive a Registration Certificate". It lets you test while the State Agency schedules your survey or CMS waits for your accreditor to confirm you.

Compliance or accreditation is the one real choice in this table. Under compliance, the State Agency or CMS surveys you. Under accreditation, one of seven CMS-approved organizations inspects you to its own standards, which CMS notes may be stricter than CLIA. Check that the accreditor covers every specialty you test: CMS's September 2026 specialty matrix shows AABB at 14 of 24 specialties and ASHI at 4 of 24, while the other five cover all 24. CAP, COLA and The Joint Commission compared covers the three most labs choose between.

CMS's first tip on its apply page is to check with your State Agency for state-specific requirements. "Some states may have additional licensing requirements. Laboratories in these states must meet both the CLIA and state requirements."

Two states run their own HHS-approved programs. CMS says a lab in New York or Washington may not need a CLIA certificate at all, and adds: "New York has a partial exemption." Labs there start with the state program CMS lists, not with Form CMS-116.

The application is Form CMS-116, "Clinical Laboratory Improvement Amendments (CLIA) Application for Certification". The current edition is (03/24), OMB No. 0938-0581, expiring 03/31/2027. It is a fillable PDF: type your answers and save it. Our walk-through covers Form CMS-116, section by section.

• Section II, one box only. Waiver labs complete Sections I–VI and IX–X; PPM labs I–VII and IX–X; compliance and accreditation labs all of I–X. Accreditation labs also tick their accreditor.
• Director proof. The form: directors "performing non-waived testing (including PPM) must meet specific education, training and experience under subpart M", and proof "must be submitted with this application." A waiver lab still names a director, with no federal qualifications required.
• Test volume. Give the current or estimated annual volume. For non-waived certificates the count leaves out waived tests and tests run for quality control, quality assurance or proficiency testing (§ 493.43(c)(3)).
• A shared email address. CMS sends the fee notice and the certificate by email, so it suggests an address "that many laboratory staff can access and use."
• One application per location, except mobile units, limited public health testing and hospital labs on one campus under common direction (§ 493.43(b)).

Send it to the State Agency for the state where the lab sits (CMS's contact list). The form's own note: "Completed 116 applications must be sent to your local State Agency. Do not send any payment with your application."

Once the State Agency processes the form, CMS emails a fee notification that carries your CLIA number. You pay on pay.gov by bank account (ACH), debit or credit card. The MLN fact sheet is plain about the old way: "payments by paper check are no longer accepted".

Compliance and accreditation labs then pay by schedule, set by annual test volume and, in the lower bands, the number of specialties. A compliance lab pays a certificate fee plus CMS's average survey fee; an accredited lab pays the same certificate fee plus a much smaller validation fee, and its accreditor's own fees on top. The first four bands:

CMS fee schedule, updated 2024, read 2026-10-23; seven more bands run up to more than 1,000,000 tests a year. The survey columns are averages, not fixed prices. CMS's footnote sends you to your State Survey Agency for the exact certificate and survey fees your lab owes. Find your band with the CLIA fee calculator.

The CLIA number is a "ten-character alpha-numeric CLIA identification number". The Medicare Claims Processing Manual (Ch. 16, § 70.4) spells out the pattern: positions 1 and 2 are the state code, position 3 is the letter D, and positions 4 to 10 are the number CMS's system assigns. A made-up example reads 12D3456789. It goes on every claim for lab services, and on every call to the State Agency or CMS.

The certificate itself arrives by email after CMS receives your payment. CMS's apply page: "You can begin testing once you receive it." The brochure adds that you should first check with your State Agency, since some states have their own requirements. You can view and reprint the certificate later on CMS's QCOR site (how to search QCOR).

The number is the start. What the lab owes from then on depends on the certificate it holds.

Certificate of Waiver

Follow "manufacturers' instructions for performing the test" (§ 493.15(e)(1)), and run nothing that is not waived until you hold the certificate for it (§ 493.39(a)). Waiver labs are "not subject to biennial inspections" (§ 493.1775(a)), but CMS or the State Agency can still come on a complaint, to check for tests beyond the certificate, over a risk of harm, or to collect information about waived tests. More in the Certificate of Waiver guide.

Certificate for PPM procedures

Microscopy stays within the nine procedures in § 493.19(c), done by a physician, midlevel practitioner or dentist during the patient's visit. Subparts H, J, K and M apply to those procedures (§ 493.47(c)(2)). None of the nine is graded in Subpart I, so the lab must verify their accuracy "at least twice annually" (§ 493.1236(c)). No routine survey, the same as waiver labs.

Certificate of Compliance

The full non-waived rule book: subparts F, H, J, K, M and Q (§ 493.20(b), § 493.25(b)). That means proficiency testing, facility administration, a quality system with quality control, qualified personnel and inspections. CMS's MLN fact sheet: "Surveys happen every 2 years at CoC laboratories" (what a CLIA inspection looks like). If a survey finds deficiencies, the brochure says you won't get your certificate until they are fixed and the fee is paid.

Certificate of Accreditation

The same CLIA requirements, met through your accreditor's program: "An AO inspects laboratories once every 2 years." CMS can still run validation and complaint inspections (§ 493.1780). You must let your proficiency testing provider (CMS-approved PT programs) send results to your accreditor (§ 493.551(b)(4)). If the accreditor withdraws, the lab keeps its certificate for 45 days after notice (§ 493.551(c)); a lab that fails its accreditor's program faces a full compliance review by CMS (§ 493.61(c)).

Every certificate lasts two years at most (§ 493.37(e), § 493.47(e), § 493.49(d), § 493.61(d)), and the fees come round on the same cycle. Three duties run in between:

Sources: § 493.39, § 493.51, § 493.53, § 493.63, § 493.37(f), § 493.49(g), § 493.61(h). Accredited labs notify the accreditor of a new specialty or method change.