To get a CLIA number, you submit a completed Form CMS-116 to your state’s survey agency. The agency enters your application into the federal system, CMS generates a bill, and once you pay, your CLIA certificate and unique identification number are mailed to you. The entire process typically takes several weeks from submission to certificate in hand. Here’s what you need to know at each step.
What a CLIA Number Is and Who Needs One
A CLIA number is a unique identifier assigned to any facility in the United States that tests human specimens for health purposes. Under the Clinical Laboratory Improvement Amendments of 1988, every site that performs lab testing to diagnose, prevent, or treat disease must be certified. This applies broadly: physician offices running strep tests, hospitals with full chemistry panels, clinics doing urinalysis, and independent labs all need their own CLIA number.
A few narrow exceptions exist. Labs that only do employment drug testing under SAMHSA certification, forensic labs working criminal cases, and research facilities that never report patient-specific results don’t need CLIA certification.
Choose the Right Certificate Type
Before you apply, you need to decide which of four certificate types fits your lab’s testing. This choice determines your fees, inspection requirements, and what tests you’re allowed to run.
- Certificate of Waiver: Covers only FDA-waived tests, which are simple, low-risk procedures like rapid strep, basic glucose monitoring, and many point-of-care tests. This is the most common certificate for small physician offices. No routine inspections are required, and there are no federal education requirements for the lab director.
- Certificate for Provider-Performed Microscopy (PPM): Allows a physician, midlevel practitioner, or dentist to perform specific microscopy procedures (like wet mounts or KOH preps) in addition to waived tests.
- Certificate of Compliance: Required for labs performing moderate or high complexity testing. CMS inspects these labs to verify they meet all applicable regulations.
- Certificate of Accreditation: Also covers moderate and high complexity testing, but the lab is inspected by a CMS-approved accreditation organization (such as the College of American Pathologists or COLA) instead of directly by CMS.
If you’re only running basic point-of-care tests, a Certificate of Waiver is the simplest and cheapest path. If your testing goes beyond that, you’ll need one of the other three.
Complete Form CMS-116
Form CMS-116 is the official CLIA application. You can download it as a PDF from the CMS website. Every applicable section must be filled out completely. Incomplete applications get returned, which adds weeks to your timeline.
For a new application, check “initial application” and leave the CLIA Identification Number field blank. Your number gets assigned during processing. The form requires:
- General information: Facility name, physical address, mailing address, federal tax ID, email, phone number, anticipated start date, and the name and credentials of your lab director.
- Certificate type: Which of the four certificates you’re requesting.
- Facility type: Whether you’re a physician office, hospital, ambulatory surgery center, pharmacy, or another category.
- Testing hours: The times during which lab testing is performed.
- Test menu details: If applying for a Certificate of Waiver, you list each waived test by analyte, test name, manufacturer, and estimated annual volume. PPM and non-waived certificates have their own corresponding sections with similar details.
- Multiple sites: If you want a single certificate to cover more than one testing location, there’s a dedicated section for that.
Do not send payment with your application. CMS bills you separately after your application is entered into the system.
Lab Director Requirements
Every CLIA-certified lab needs a designated director, but the qualifications vary dramatically depending on your certificate type. For a Certificate of Waiver, there are no federal education or experience requirements for the director. For anything beyond waived testing, the requirements are substantial.
A lab director for moderate complexity testing must be a licensed physician with at least one year of lab supervisory experience, or hold a doctoral, master’s, or bachelor’s degree in a laboratory science field with progressively more experience required at lower degree levels. Someone with a bachelor’s degree, for example, needs at least two years of hands-on lab training plus two years of supervisory experience in non-waived testing. All non-physician directors also need at least 20 continuing education credit hours in laboratory practice.
Proof of these qualifications, including diplomas, transcripts, and credentials, must be submitted with your CMS-116 form. If the director attended a foreign school, an equivalency evaluation of their education is required. Missing documentation delays processing.
Where to Submit Your Application
Mail your completed CMS-116 and supporting documents to your state’s survey agency. CMS publishes a PDF directory of state agency contacts on its website. The state agency reviews and enters your application into the CMS system.
Two states handle things differently. In New York, non-physician office laboratories should contact the New York State Department of Health directly at (518) 485-5378 before applying. In Washington, applicants should call the state agency at 253-395-6746 for guidance. Labs outside the U.S. and its territories must email CMS about the international certification process before submitting the form.
Many states also have their own laboratory licensing laws on top of CLIA. Contact your state agency to find out whether you need to submit additional forms or meet extra requirements.
Fees by Certificate Type
CLIA fees depend on which certificate you’re getting and, for compliance and accreditation certificates, how many tests your lab performs annually.
A Certificate of Waiver costs $248. A PPM certificate costs $297. These are flat fees regardless of volume. For a Certificate of Compliance or Accreditation, fees are tiered by annual test volume and number of specialties. A low-volume lab running 2,000 or fewer tests per year pays $223 for the certificate itself plus a $446 compliance fee. At the other end, a high-volume lab running over a million tests annually pays $11,801 for the certificate plus $5,459 in compliance fees, with additional charges for every 500,000 tests beyond that.
All certificates also carry a registration fee. For waived certificates, the initial registration and processing fee is $150. For compliance and accreditation certificates, registration is $123.
How Long It Takes
The timeline from submission to receiving your certificate involves several steps that each add days or weeks. After your state agency enters the application into the CMS system, a batch program runs the following Tuesday night to detect new applications. It then generates a bill, which takes up to 10 days to print and mail, plus 2 to 7 days for postal delivery.
Once you pay, the system picks up your payment during the next Tuesday night batch run, then generates and mails your certificate on the same timeline: up to 10 days for printing and mailing, plus postal delivery time. From start to finish, you’re looking at roughly 4 to 6 weeks under normal conditions, assuming no delays from incomplete paperwork or missing director credentials. Some state agencies process applications faster than others, so your mileage will vary.
Keeping Your Certificate Active
Every CLIA certificate, regardless of type, is valid for no more than two years. CMS sends you a written notice before expiration with instructions on the renewal fee amount and where to pay. Your renewed certificate won’t be issued until payment is received, so don’t let it lapse. Operating without a valid CLIA certificate means you cannot legally perform or bill for lab testing.
The renewal fee is based on the fee schedule in effect at the time your renewal is processed, not when your original certificate was issued. If fees have increased in the two years since your last certificate, you’ll pay the updated amount. If your lab changes the types of tests it performs or its annual volume shifts significantly, you may also need to update your certificate type, which can affect your fee category.