What Is CLIA? The Clinical Laboratory Improvement Amendments Explained

The CLIA law and regulations

• The law. CLIA '88 amended the Public Health Service Act. It was enacted as Public Law 100-578 (102 Stat. 2903) and is codified at 42 USC 263a. CDC's CLIA overview notes that the law has been amended twice since 1988: by the Food and Drug Administration Modernization Act of 1997 and by the Taking Essential Steps for Testing Act of 2012. It is still cited as CLIA '88.

• The regulations. CMS issues the rules in 42 CFR Part 493, "Laboratory Requirements". According to CDC, the final CLIA regulations were published in 1992, phased in through 1994, and amended in 1993, 1995, and 2003. Later rules, such as the personnel changes effective December 28, 2024, also amended Part 493. See CLIA personnel rule changes.

• The interpretive guidelines. CMS publishes survey procedures and interpretive guidance in Appendix C of the State Operations Manual. Surveyors use it, and labs use it to interpret the rules.

To search past Federal Register notices and older CFR editions, use CDC's CLIA documents database.

Who CLIA covers, and what it exempts

Under 42 CFR 493.3, a laboratory is out of compliance unless it has a current CLIA certificate for the testing it performs or is CLIA-exempt. Waived testing is included. A site that runs only waived tests still needs a Certificate of Waiver.

The rules do not apply to:

• facilities, or parts of facilities, that only perform forensic testing,

• research labs that do not report patient-specific results for diagnosis, prevention, treatment, or health assessment, and

• drug testing that a SAMHSA-certified lab performs under SAMHSA guidelines. All other testing at that lab is still covered.

Federal laboratories are covered, but HHS may modify how the requirements apply to them (§ 493.3(c)).

"CLIA-exempt" describes a lab, not a test. It means a lab licensed by a state whose program CMS has approved as equal to or more stringent than CLIA (§ 493.2). See CLIA-exempt states.

CMS vs. FDA vs. CDC: who does what under CLIA

The FDA's CLIA page and CDC's CLIA overview describe three federal agencies, each with its own role.

• CMS: Issues certificates and collects user fees. Conducts inspections and enforces compliance. Approves accreditation organizations and state exemptions. Monitors proficiency testing (PT) performance and approves PT programs. Publishes CLIA rules and guidance.

• FDA: Categorizes tests by complexity. Reviews CLIA Waiver by Application requests. Develops rules and guidance for complexity categorization.

• CDC: Provides analysis, research, and technical assistance. Develops technical standards and practice guidelines, including for cytology. Runs lab quality improvement studies and monitors PT practices. Develops educational resources. Manages the Clinical Laboratory Improvement Advisory Committee (CLIAC).

On a day-to-day basis, most labs deal with their State Survey Agency, which works for CMS, or with their accreditation organization. The CMS CLIA page tells labs to contact their State Agency about fees, CMS-116 applications, certificate status or upgrades, and director changes. CDC states that it does not issue CLIA certificates or process fee payments.

CLIA test complexity: waived, moderate, high

Under 42 CFR 493.5, every test falls into one of three categories:

1. Waived: tests listed in § 493.15(c), tests cleared for home use, and tests FDA waives by application. According to CDC's test complexity page, waived-only sites must hold a CLIA certificate and follow the manufacturer's instructions. Other CLIA requirements do not apply to them.

2. Moderate complexity, including the PPM (provider-performed microscopy) subcategory.

3. High complexity.

FDA scores each nonwaived test on the seven criteria in 42 CFR 493.17. Each criterion gets a score of 1 to 3. A total of 12 or less is moderate complexity, and a total above 12 is high complexity. CDC notes that tests developed by a lab, or modified from the manufacturer's instructions, default to high complexity. It also notes that moderate and high complexity standards differ only in personnel requirements.

To find a test's category, check the package insert or FDA's CLIA categorization database. SLC's CLIA certificate types and test complexity guide explains how complexity maps to certificates.

The five CLIA certificate types

Under § 493.5(c), a lab must be CLIA-exempt or hold one of these certificates:

• Certificate of Waiver: waived tests only. See CLIA Certificate of Waiver requirements.

• Certificate for PPM Procedures: PPM procedures plus waived tests.

• Registration Certificate: lets a nonwaived lab test until it is surveyed for compliance.

• Certificate of Compliance: issued after a State Agency survey finds the lab compliant.

• Certificate of Accreditation: for labs accredited by a CMS-approved accreditation organization.

You apply for any of these with Form CMS-116. See how to fill out the CMS-116.

What nonwaived CLIA compliance involves

Labs doing moderate or high complexity testing must be inspected and must meet the CLIA quality standards. Per CDC, these include proficiency testing, quality control and assessment, and personnel requirements. In Part 493, these are:

• Subpart H: proficiency testing.

• Subpart J: facility administration.

• Subpart K: the quality system, including quality control.

• Subpart M: personnel.

• Subpart Q: inspection.

CLIA basics checklist

1. ☐ List every test on your menu and its complexity category (package insert or FDA database).

2. ☐ Confirm whether any testing falls under a § 493.3 exception (forensic, non-reported research, SAMHSA drug testing).

3. ☐ Confirm whether your state is CLIA-exempt (New York or Washington).

4. ☐ Choose the certificate that matches your highest-complexity testing.

5. ☐ File Form CMS-116 with your State Agency, and pay fees online once CMS emails your fee coupon.

6. ☐ Keep a valid email address on file with CMS. CLIA certificates and fee coupons are now electronic.

7. ☐ For nonwaived testing, staff the required roles under Subpart M and set up PT, QC, and quality assessment before patient testing.

8. ☐ Bookmark 42 CFR 493, SOM Appendix C, and the CMS, FDA, and CDC CLIA pages.

CMS resources for clinical labs

• CMS MLN006270: CLIA Program & Medicare Lab Services: CMS's overview of CLIA certificates and Medicare lab claims.

• CMS Clinical Labs Information Center: CMS's hub for lab payment, coverage, and billing.

Related SLC guides: - Medicare lab billing basics - Medicare Clinical Laboratory Fee Schedule (CLFS) - PAMA reporting for clinical laboratories - Medicare lab NCDs and LCDs

FAQs

What does CLIA stand for?

Clinical Laboratory Improvement Amendments, passed by Congress in 1988 and often written as CLIA '88.

Who enforces CLIA?

CMS enforces CLIA, mostly through State Survey Agencies and CMS-approved accreditation organizations. FDA categorizes tests, and CDC provides technical support and manages CLIAC.

Do waived tests need a CLIA certificate?

Yes. A site that performs only waived tests needs a Certificate of Waiver and must follow the manufacturer's instructions.

Does CLIA apply to research labs?

Not to research testing whose patient-specific results are not reported for diagnosis, prevention, treatment, or health assessment (§ 493.3(b)(2)). If results are reported for patient care, CLIA applies.

Does CDC issue CLIA certificates?

No. CDC says it does not issue CLIA certificates or process fee payments. Contact your State Agency.

Is CLIA the same as accreditation by COLA, CAP, or The Joint Commission?

No. Accreditation by a CMS-approved organization is one way to meet CLIA. Those labs hold a Certificate of Accreditation. See CLIA, CAP, COLA, and TJC regulations.

Where are the CLIA regulations?

In 42 CFR Part 493 on eCFR, with CMS interpretive guidance in State Operations Manual Appendix C.

Get help with CLIA

SLC helps clinical laboratories nationwide choose the right certificate, file the CMS-116, and build compliant nonwaived programs. See how to start a clinical laboratory or work with a CLIA consultant.

Sound Lab Consultants Mailing address: PO Box 2135, Chandler, AZ 85244