To get a CLIA Certificate of Waiver, download the CMS-116 from the CMS forms library, complete Sections I through VI and Sections IX and X, and mail the signed form to the state agency for the state where your lab is physically located; a $180 fee coupon follows once the agency processes your application.1Centers for Medicare & Medicaid Services. How to Apply for a CLIA Certificate, Including International Laboratories2Centers for Medicare & Medicaid Services. Clinical Laboratory Improvement Amendments of 1988 (CLIA) Application for Certification The CLIA waiver application CMS-116 is free to download, and payment is never sent with the form.
Confirm Every Test You Plan to Run Is Waived
A Certificate of Waiver authorizes only tests that meet the federal definition of “waived” under 42 CFR 493.15: cleared by the FDA for home use, simple enough that erroneous results are negligible, or posing no reasonable risk of harm if performed incorrectly.3eCFR. 42 CFR 493.15 – Laboratories Performing Waived Tests Rapid strep, urine dipsticks, blood glucose, hemoglobin A1c point-of-care analyzers, rapid influenza and COVID-19 antigen tests, and prothrombin time devices are typical examples.4Centers for Disease Control and Prevention. Waived Tests
Check each test system against the FDA’s “CLIA — Currently Waived Analytes” database before you list it on the form.5Food and Drug Administration. Public Databases If a single test on your list is moderate or high complexity, a Certificate of Waiver will not cover your operation and you need a different certificate type.
What to Have in Front of You Before You Start
- Federal Tax Identification Number for the legal entity that owns or operates the lab. A solo practitioner using an SSN for tax purposes enters that.
- Physical facility address (this determines your state agency) and a separate mailing address if applicable.
- Laboratory Director’s full legal name, phone, and credentials. Waived testing does not require you to submit proof of the director’s qualifications; that documentation applies to non-waived testing only.6Centers for Medicare & Medicaid Services. Clinical Laboratory Improvement Amendments (CLIA) Application for Certification
- Specific waived test systems you will run, plus an estimated total annual test volume across all of them.
- Days and hours of laboratory testing.
Filling Out the Form Section by Section
For a Certificate of Waiver, the instructions direct you to Sections I through VI and Sections IX and X. Sections VII and VIII apply to provider-performed microscopy and non-waived testing; leave them blank.6Centers for Medicare & Medicaid Services. Clinical Laboratory Improvement Amendments (CLIA) Application for Certification
Section I: General Information
Check “Initial Application” if this is your first CLIA filing, and leave the CLIA number blank. If you already hold a different CLIA certificate and are switching to a waiver, check “Change in Certificate Type” and enter the effective date. Fill in the facility name, TIN, contact information, physical address, and the Laboratory Director’s name and credentials.
Section II: Type of Certificate Requested
Select “Certificate of Waiver.” This one checkbox drives your regulatory tier, your fee, and whether your lab is subject to routine inspections. Waived labs are exempt from the routine compliance inspections that apply to labs holding a Certificate of Compliance or Accreditation.7eCFR. 42 CFR 493.643 – Fee for Determination of Program Compliance
Section III: Type of Laboratory
Pick the single category that best describes your facility from options such as physician office, ambulatory surgery center, community clinic, skilled nursing facility, home health agency, pharmacy, and industrial lab. Only one selection is allowed.
Section IV: Hours of Laboratory Testing
Enter the days and hours during which testing occurs. An incomplete Section IV is a routine reason state agencies bounce applications back.
Section V: Multiple Sites
Most applicants check “No.” If you operate from more than one location, see the multi-site rules below before completing this section.
Section VI: Waived Testing
List every waived test the lab will perform and enter your estimated total annual test volume for all waived tests combined. If you later add a waived test not on the original list, update your state agency.
Section IX: Type of Control
Indicate whether the lab is voluntary nonprofit, for-profit, or government-operated, and disclose any foreign ownership.
Section X: Director Affiliation
If your Laboratory Director also directs other CLIA-certified labs, list those facilities and their CLIA numbers. Otherwise leave it blank.
The owner or Laboratory Director must sign and date the form. An unsigned CMS-116 will be returned.
Where to Send It
Mail the completed CMS-116 to the state agency for the state where your testing facility is physically located. CMS publishes a directory of state agency addresses and phone numbers.8Centers for Medicare & Medicaid Services. State Agency and CLIA Operations Branch Contacts Do not send the form to CMS headquarters; it will not be processed there.
Some states require a separate state-level laboratory license or application on top of the federal CMS-116, with fees that vary. Confirm state-level requirements with your state agency before you submit.
Washington and New York Applicants
Labs in Washington and New York do not file the federal CMS-116. Both states run CLIA-exempt programs that CMS has approved as equivalent to federal standards.9Centers for Medicare & Medicaid Services. List of Exempt States Under the Clinical Laboratory Improvement Amendments (CLIA) In Washington, apply for a Medical Test Site license through the state Department of Health; that license serves as your CLIA number.10Washington State Department of Health. Medical Test Sites – Licensing Information In New York, register through the Clinical Laboratory Evaluation Program at the state Department of Health, which classifies waived-only facilities as “limited service laboratories.”11New York State Department of Health, Wadsworth Center. About the Program
Fees and Payment Timing
Do not include any payment with your CMS-116. After the state agency processes your application, CMS mails a fee remittance coupon showing your newly assigned ten-digit CLIA identification number and the amount due. The biennial fee for a Certificate of Waiver is $180, covering a two-year period.12Centers for Medicare & Medicaid Services. CLIA Certificate Fee Schedule Send payment to the lockbox address printed on the coupon. Your certificate is not issued until payment clears.
Waived labs are exempt from the separate compliance-determination fee that applies to labs undergoing routine inspection.7eCFR. 42 CFR 493.643 – Fee for Determination of Program Compliance The $180 certificate fee is the only federal CLIA cost for a waived lab in each two-year cycle.
After the Certificate Arrives
You cannot legally perform testing or bill for laboratory services until the certificate is in hand. CMS states that testing begins only after the certificate is received.13Centers for Medicare & Medicaid Services. How to Obtain a CLIA Certificate Post the certificate in a visible location at the testing site.
Billing With the QW Modifier
On Medicare and Medicaid claims, most waived tests require the HCPCS modifier “QW” appended to the procedure code (for example, 80047QW). A small set of tests are recognized as waived without the QW modifier, including urine dipstick (81002), urine pregnancy (81025), and blood glucose (82962).14Centers for Medicare & Medicaid Services. New Waived Tests A claim missing the QW modifier when required will be denied. Your CLIA number must appear on every laboratory claim; payer systems cross-check the certificate level against the test billed.
Records
Keep quality control records, patient test results, and instrument printouts for at least two years. Original test reports, including final, preliminary, and corrected versions, must be retained or retrievable for at least two years from the reporting date. Pathology reports carry a ten-year retention period.15eCFR. 42 CFR 493.1105 – Standard: Retention Requirements
Multiple Sites, Mobile Units, and Hospital Campuses
Each testing location generally needs its own certificate and its own CMS-116. Three exceptions allow a single application to cover multiple sites:16eCFR. 42 CFR 493.35 – Application for a Certificate of Waiver
- Mobile units and temporary locations, such as mobile vans, health fairs, and pop-up testing events, can operate under a designated primary site’s certificate and address.
- Not-for-profit and federal, state, or local government labs that perform no more than a combined 15 moderately complex or waived tests per certificate may file a single application.
- Hospital laboratories occupying contiguous buildings on the same campus under common direction may file a single application.
If one of these applies, complete Section V and describe the arrangement. Mobile operations must identify the permanent base of operations where records are stored.
Renewal and Required Change Notifications
A Certificate of Waiver is valid for two years. CMS mails a recertification package before expiration. To renew, check “Survey” on the new CMS-116 (the form instructions designate that box for recertification), return it to your state agency, and pay the $180 fee once the coupon arrives.6Centers for Medicare & Medicaid Services. Clinical Laboratory Improvement Amendments (CLIA) Application for Certification
Report the following changes to your state agency within 30 days:1Centers for Medicare & Medicaid Services. How to Apply for a CLIA Certificate, Including International Laboratories
- Change in ownership, so the new legal entity is properly registered.
- New Laboratory Director, identified by name and effective date on a new CMS-116 or written notification.
- Change of physical address, which can shift oversight to a different state agency and may require a new application.
- Change of the facility’s legal name.
Failing to report these changes can lead to certificate suspension or civil money penalties.