CLIA Certification Guide for Laboratories

This Quick Start Guide provided by CMS offers guided instructions for laboratories on the following processes:

1. Completion of the CLIA application form, CMS-116
2. Identification of the appropriate State Agency for form submission
3. Fee coupon & applicable fees
4. Receipt of laboratory certificate and commencement of testing
5. Maintaining your CLIA certificate

Applying for a New CLIA Certificate

1. Determine the required type of CLIA certificate. There are four types:

• • Certificate of Waiver: Authorizes tests granted waived status by the FDA.
    • Cost: $180.00 every two years.
  • Certificate of Microscopy (PPM): Allows the provider to conduct microscopic procedures using a microscope. The laboratory may also perform waived tests under a PPM certificate.
    • Cost: $240.00 every two years.
  • Certificate of Compliance: For laboratories conducting waived, PPM, and non-waived tests.
    • Cost: varies based on annual non-waived test volume.
  • Certificate of Accreditation: For laboratories conducting waived, PPM, and non-waived tests, choosing to be accredited by an approved organization.
    • Cost: based on annual test volume (in addition to accreditation fee).

2. Complete all sections of the CMS 116 CLIA Application. Include a list of all tests performed and an estimated test volume on page 3. An email address is essential for timely communication. 

3. Provide director credentials:

• • Certificate of Waiver: No director credentials required.
  • Certificate of Provider Performed Microscopy: Submit copy of director’s medical license.
  • Certificate of Compliance: Submit copy of director’s medical license or other qualifying information.
  • Certificate of Accreditation: Submit copy of director’s medical license or other qualifying information.

4. Email the completed application to your State Agency.

5. Upon processing, a confirmation letter should be sent to you within 5-7 business days.

6. Following application entry into the federal system, a fee coupon will be generated and mailed by a federal contractor.

7. Upon payment processing, the new CLIA certificate will be printed and mailed via US Mail from the federal contractor. Upon receipt, the laboratory may commence testing and billing for the performed tests.

Please check with your state agency as these instructions may vary from state-to-state. 

Modifying your CLIA Certificate

Certain changes necessitate completion of a CMS 116 CLIA Application, mainly Name, Address, Tax ID, or Phone Changes. To make changes, inform your State Agency and include the following:

• • Laboratory Name
  • CLIA number
  • Names of Laboratory Director and Owner
  • Details of the change(s) – old information, new information, and effective date
  • Signature of the Laboratory Director or authorized designee Alternatively, submitting a new CMS 116 CLIA Application is acceptable.

Laboratory Director Changes

• • Certificate of Waiver: Submit written notification including CLIA number, facility name/address, old/new director details, and effective date, signed by the new director. In some cases, an updated CMS-116 may be requested.
  • Certificate of Provider Performed Microscopy (PPMP): Complete all sections of the CMS-116 CLIA application and provide the new director’s medical license copy.
  • Certificate of Compliance: Complete all sections of the CMS-116 CLIA application and provide the new director’s credentials, including medical license copy if applicable.
  • Certificate of Accreditation: As of January 2019, director changes for Certificate of Accreditation labs are processed by the Accrediting Organization.

Certificate Type Changes

• For certificate type changes, complete and sign all sections of the CMS 116 CLIA Application and submit the application to your State Agency.

Adding a Test/Specialty

• • Certificate of Waiver: Written notification required, specifying CLIA number, facility details, tests to be added, and effective date. No confirmation letter is issued.
  • Certificate of Compliance: Submit CMS-116 within 6 months of any deletions or changes in test methodologies.
  • Certificate of Accreditation: Notify the accreditation program within 6 months of any deletions or changes in test methodologies.

Keep in mind that a new CLIA certificate is not issued for changes. Confirmation letters are only sent for director or tax identification number changes. For other changes, an automatic receipt acknowledgment is sent.

Payment Procedure for CLIA Certificate

• Payments by mail: Send to CLIA Laboratory Program, PO Box 3056, Portland, OR 97208-3056. Make check payable to “CLIA Laboratory Program” and indicate CLIA number on the memo line.
• Online payments: Visit www.pay.gov, search for “CLIA,” continue through the prompts, complete the form, and retain the confirmation number.

Terminating your CLIA Certificate

• Provide written notification, including CLIA number, facility details, termination effective date, and reason, signed by the laboratory director. Send to your State Agency.

More CLIA Resources

• Centers for Disease Control (CDC)
• Centers for Medicare & Medicaid Services (CMS)
• Food & Drug Administration
• CDC Resources for Provider-Performed Microscopy (PPM) Testing
• CDC Resources for Waived Testing
• Michigan Laboratory Resources through Licensing & Regulatory Affairs (LARA)