Before you start: which sections must you complete?
Section II of the form tells you which sections to fill in:
Certificate of Waiver: complete Sections I–VI and IX–X.
Certificate for Provider Performed Microscopy Procedures (PPM): complete Sections I–VII and IX–X.
Certificate of Compliance: complete Sections I–X.
Certificate of Accreditation: complete Sections I–X, plus the accreditation organization.
The form says it plainly: "ALL APPLICABLE SECTIONS OF THIS FORM MUST BE COMPLETED." The instructions add that incomplete applications "cannot be processed and will be returned to the facility." CMS says to download the fillable PDF, type your answers, save it as a PDF, and give information as of the date you complete it (Quick Start Guide).
Not sure which certificate fits your test menu? See our guide to starting a clinical laboratory.
Section I: General Information
Application type
Check one box:
Initial Application: for a first-time applicant. Also enter the Anticipated Start Date.
Survey: for an initial survey or a recertification.
Change in Certificate Type: give the effective date.
Change in Laboratory Director or Other Changes (Specify): for example a new location, a new director, or a lab closure. Give the effective date.
CLIA Identification Number
If this is an initial application, leave it blank. The number is assigned when the application is processed. Everyone else enters the 10-character CLIA number on their current certificate.
Facility Name and Federal Tax Identification Number
Be specific with the facility name, especially when the lab is part of a larger entity. The instructions give the example "respiratory therapy department in XYZ Hospital," and note that a physician office may use the physician's name. Whatever you enter here is what appears on your certificate. Enter the facility's Federal Tax Identification Number (EIN) in the field next to it.
Email, telephone and fax
CMS uses this email address to communicate with your lab. Checking "Receive notifications including electronic certificates via email" means you must enter a valid email address. CMS says that after March 1, 2026 it sends all fee coupons and CLIA certificates by email, and it suggests a business address that several staff members can access (Quick Start Guide).
Facility Address
This field is required. It must be the physical location where testing is performed. You can include a building, floor, suite or room, but it cannot be a P.O. Box or Mail Stop.
Mailing/Billing and Corporate addresses
The form still has optional mailing and corporate address fields, plus "send fee coupon / send certificate to" checkboxes. The March 2026 Quick Start Guide says these fields and checkboxes "are no longer required and may be left blank," because fee coupons and certificates now arrive by email.
Director name, phone and credentials
Enter the laboratory director's name (Last, First, Middle Initial), phone number and credentials. Leave the "For Office Use Only / Date Received" box blank.
Section II: Type of Certificate Requested (check only one)
Choose based on the highest complexity of testing your lab performs:
Certificate of Waiver: waived tests only.
Certificate for PPM: PPM procedures, or PPM plus waived tests.
Certificate of Compliance: waived, PPM, and moderate and/or high complexity tests. The State Agency surveys the lab against CLIA standards.
Certificate of Accreditation: the same range of testing, but the lab is accredited by a CMS-approved accreditation organization. The form lists The Joint Commission, ACHC, AABB, A2LA, CAP, COLA and ASHI.
Two requirements printed on the form:
Director qualifications. "Laboratory directors performing non-waived testing (including PPM) must meet specific education, training and experience under subpart M of the CLIA regulations. Proof of these qualifications for the laboratory director must be submitted with this application." The instructions list what to send: state licensure (if applicable), diploma and transcript, credentials, and laboratory experience. Directors who went to school outside the U.S. need a credential evaluation showing U.S. equivalency. The instructions warn that leaving any of this out "will delay the processing of your application." (Need a qualified director? See laboratory director services.)
Accreditation evidence. A Certificate of Accreditation applicant must provide evidence of accreditation, or of having applied for accreditation, "within 11 months after receipt of your Certificate of Registration."
Use the FDA CLIA test categorization database to look up each test system's complexity.
Section III: Type of Laboratory
Check the one code that best describes where testing happens. The codes run from 01 Ambulance through 29 Other (Specify), and include 14 Hospital, 15 Independent, 19 Mobile Laboratory, 20 Pharmacy, 21 Physician Office and 22 Practitioner Other. The instructions explain:
19 Mobile Laboratory means "a movable, self-contained operational laboratory with its own personnel, equipment, and records." Attach a separate sheet listing the VINs of every vehicle used.
22 Practitioner Other covers practitioners such as dentists and chiropractors.
Section IV: Hours of Laboratory Testing
For each day from Sunday to Saturday, enter only the hours when testing is actually performed, in HH:MM format. The instructions say "Do not use military time." If you test around the clock, check the 24/7 box. For multiple sites, attach the hours for each one in the same format.
Section V: Multiple Sites
Answer No to cover a single location and skip to Section VI. Answer Yes only if you meet one of the three regulatory exceptions on the form (42 CFR 493.35(b), 493.43(b) and 493.55(b)):
Not at a fixed location: a lab that moves between testing sites, such as a mobile unit, health screening fairs or other temporary sites, covered under the home base's certificate and address. Attach a list of the temporary sites, plus VINs for any mobile units.
Limited public health testing: a not-for-profit or Federal, State or local government lab doing no more than a combination of 15 moderate complexity or waived tests per certificate. List each site's name, address and tests.
Hospital campus: several labs in contiguous buildings on the same campus, at the same physical location or street address, under common direction. List each site or department, its location in the hospital, and its specialties or subspecialties.
The instructions also note that hospice and home health agencies "could qualify for an exception."
Section VI: Waived Testing
List each waived analyte/test, the test name and the manufacturer. The form's example is "Streptococcus group A / Ace Rapid Strep Test / Acme Corporation." Enter the estimated total annual test volume for all waived tests, or check "no waived tests are performed." The instructions count dipstick urinalysis here. If you're applying only for a Certificate of Waiver, skip Sections VII and VIII.
Section VII: PPM Testing
Check each PPM procedure you'll perform. The form lists the only ones allowed under a PPM certificate:
direct wet mounts
KOH preparations
pinworm examinations
fern tests
post-coital direct qualitative examinations
urine sediment examinations
nasal smears for granulocytes
fecal leukocyte examinations
qualitative semen analysis (presence or absence of sperm and motility only)
Enter the estimated total annual PPM volume. Labs applying for Compliance or Accreditation also include PPM volume in Section VIII.
Section VIII: Non-Waived Testing (including PPM)
Fill this in only for a Certificate of Compliance or Accreditation.
List each analyte/test, test name, manufacturer, and M (moderate) or H (high) complexity.
Check each specialty/subspecialty you test in and give its estimated annual volume. Examples include Bacteriology 110, General Immunology 220, Routine Chemistry 310, Urinalysis 320, Endocrinology 330, Toxicology 340, Hematology 400, ABO Group & Rh Group 510, Histopathology 610, Cytology 630 and Clinical Cytogenetics 900. Then give the total estimated annual test volume. For multiple sites, the total covers all sites.
If you're applying for Accreditation, write the accreditation organization next to each specialty.
Don't count tests not subject to CLIA, waived tests, QC, calculations, QA or proficiency testing.
Counting rules from the instructions' "Guidelines for Counting Tests for CLIA":
Chemistry: each non-calculated analyte is a separate test. A lipid panel of total cholesterol, HDL, LDL and triglycerides counts as 4.
Hematology: each measured CBC analyte counts separately. The WBC differential counts as one.
Microbiology: each culture request per specimen counts as one, whatever the workup. Susceptibility counts as one per antibiotic group per organism.
Urinalysis: a dipstick counts as one test regardless of the number of pads. Microscopic and macroscopic exams each count as one.
Histopathology: count per block, not per slide.
Cytology: count per slide, not per case.
Your volume and number of specialties set your fee schedule, so count carefully.
Section IX: Type of Control
Check the ownership type that fits best:
Voluntary Nonprofit: 01 Religious Affiliation, 02 Private Nonprofit, 03 Other Nonprofit
For Profit: 04 Proprietary
Government: 05 City, 06 County, 07 State, 08 Federal, 09 Other Government (specify)
Then answer whether the facility is partly or fully owned or controlled by a non-U.S. government or entity, and if so, name the country.
Section X: Director Affiliation with Other Laboratories
If the director also directs other separately certified labs, including Certificate of Waiver labs, list each one's CLIA number and name. The instructions note that for PPM, Compliance or Accreditation certificates, one person can direct no more than five certificates.
Signature block
Print the director's name and the owner's name. The owner or director signs in ink or with a secure electronic signature, and dates it. Signing means agreeing to the consent statement: the lab will operate under CLIA standards and will allow HHS to inspect the lab and its records "at any reasonable time." The form also warns that an intentional CLIA violation can bring fines and/or imprisonment.
Common CMS-116 mistakes
Using a P.O. Box as the facility address. It must be the physical testing location. (A P.O. Box is acceptable only in the optional mailing or corporate fields.)
Entering a CLIA number on an initial application. Leave it blank.
Requesting the wrong certificate. Base it on your highest-complexity test, confirmed in the FDA database.
Leaving out director qualification documents for PPM, Compliance or Accreditation. This delays processing.
Leaving out or miscounting annual test volume. Reminder #1 on the form is to include it.
Using an unmonitored or wrong email address. Fee coupons and certificates now come by email.
Using military time in Section IV, or listing clinic hours rather than testing hours.
Skipping Section V or the attachments for mobile sites (VINs, temporary site lists).
Sending money with the application. The form says: "Do not send any money with your application."
Not checking for state requirements. CMS notes some states require extra forms. Ask your State Agency.
Where to submit the CMS-116 and how fees are paid
Send the completed form to the State Agency for the state where the lab is located, not to CMS. The CMS CLIA State Agency contact list (PDF) gives each agency's address, email and fax. Ask your agency how it accepts applications (for example, by email or mail).
Fees are billed after the form is processed:
CMS emails a fee coupon with your 10-character CLIA ID and the total due. The amount depends on certificate type and test volume (see the CLIA Certificate Fee Schedule).
From March 1, 2026, CLIA is paperless. CMS no longer mails paper coupons or certificates and no longer accepts paper checks. You pay on pay.gov by ACH, debit or credit card, and payments process overnight (CMS Paperless FAQ, Quick Start Guide).
Coupons and certificates come from noreply-cms-ccsq@ccsq.cms.hhs.gov. Add that address to your safe senders list. If nothing arrives, check spam, then contact your State Agency.
CMS warns that third parties have mailed fake "CLIA invoices." Official CLIA communications come only from CMS or your State Agency.
Paperless certificates and coupons don't apply in CLIA-exempt states.
What happens after you submit
The State Agency processes the form and assigns your CLIA number.
You get the fee coupon by email. For Compliance and Accreditation applicants, the coupon includes the compliance (survey) or validation fee where applicable.
Your certificate is issued.
Waiver and PPM labs get their certificate after paying.
Compliance and Accreditation applicants first pay for and get a Certificate of Registration. It lets you do non-waived testing (and waived testing) until you're surveyed or your accreditation is verified. It is valid for no more than 2 years.
Survey. A lab holding a Certificate of Registration "typically" has its initial survey within the first year. After that, Compliance and Accreditation labs are surveyed every 2 years. Waiver and PPM labs are "not routinely surveyed," but by signing the form you agree to inspection at any reasonable time.
Keep it current. All CLIA certificates are valid for 2 years. Report changes to your State Agency:
Ownership, name, location or director changes: within 30 days.
Testing changes: within 6 months for Registration, Compliance and Accreditation labs. Waiver and PPM labs must notify immediately, before testing outside their certificate.
You can look up and reprint your certificate through the CLIA Certificate Lookup on QCOR.
CDC resources on CLIA
CDC's overview of the CLIA program: CDC explains that CLIA applies to every U.S. site that tests human specimens to assess health or to diagnose, prevent, or treat disease. It also explains that CDC supports the program alongside CMS and FDA.
CDC on CLIA test complexity categories: CDC explains how FDA scores tests as moderate or high complexity using seven criteria. It also notes that lab-developed or modified tests default to high complexity, and that moderate and high complexity standards differ only in personnel requirements.
CDC on provider-performed microscopy (PPM): CDC describes PPM as a limited set of moderate complexity microscopy tests that a PPM certificate allows, along with waived tests.
CMS resources for clinical labs
CMS MLN006270: CLIA Program & Medicare Lab Services: How the CLIA certificate and the 10-character CLIA number tie into Medicare lab claims.
CMS Clinical Labs Information Center: CMS's hub for lab payment, coverage, and billing resources.
Related SLC guides:
CMS-116 FAQs
Where do I get the current CMS-116 form?
Download it from cms.gov: Form CMS-116 PDF. The current version is marked "Form CMS-116 (03/24)," OMB No. 0938-0581, expiring 03/31/2027.
Do I send the CMS-116 to CMS?
No. Send it to your state's CLIA State Agency, found on the CMS State Agency list.
Do I include payment with the application?
No. The form says not to send money. You'll get an emailed fee coupon and pay on pay.gov. Since March 1, 2026, checks are no longer accepted.
What do I enter for the CLIA number on a new application?
Nothing. Initial applicants leave it blank, and the number is assigned when the form is processed.
Can I use a P.O. Box?
Not for the facility address, which must be where testing happens. The optional mailing and corporate fields may use a P.O. Box, and CMS now says those fields may be left blank.
Which sections do I fill out for a Certificate of Waiver?
Sections I–VI and IX–X. Leave out PPM (VII) and non-waived testing (VIII).
What documents go with the application?
For PPM, Compliance or Accreditation, include proof of the director's qualifications: state licensure if applicable, education (diploma, transcript, foreign equivalency), credentials and lab experience. Ask your State Agency whether your state requires anything else.
How long is a CLIA certificate valid?
Two years. A Certificate of Registration is valid for no more than 2 years while you wait for a survey or accreditation verification.
Get your CMS-116 right the first time
Sound Lab Consultants helps labs across the country choose the right certificate, count test volume, document director qualifications and prepare for the survey that follows. See our CLIA consultant services and how to start a clinical laboratory.
We can review your CMS-116 before you submit it.
Sound Lab Consultants (SLC) works with labs nationwide. Mailing address: PO Box 2135, Chandler, AZ 85244.
Sources: Form CMS-116 (03/24) and Instructions; CMS CLIA Certification Quick Start Guide (March 2026); CMS Paperless FAQ; CMS Apply for a CLIA Certificate page; CMS CLIA Certificate Fee Schedule; CMS CLIA State Agency Contacts. This page summarizes official CMS material and is not a substitute for the form instructions or 42 CFR Part 493.
Sound Lab Consultants provides lab director and technical consultant services, inspection readiness and mock surveys, deficiency and sanctions response, new lab startup, and waived-to-moderate/high complexity upgrades.