Which sections of the CMS-116 do I fill out for a Certificate of Waiver?

Sections I through VI and IX through X, according to Section II of the form. Sections VII (PPM) and VIII (nonwaived testing) are skipped unless you are applying for those certificate types.

Can I use a P.O. box on the CMS-116?

Not for the facility address. The instructions say it must be the physical location where testing is performed and cannot be a Post Office box or Mail Stop. Since March 2026 CMS sends coupons and certificates by email, so the email field matters more than any mailing address.

Do I send the CLIA fee with the CMS-116?

No. The form says not to send any payment with the application. After the State Agency processes it, CMS emails a fee coupon and the lab pays on pay.gov.

Who can sign the CMS-116?

An owner or an authorized representative of the laboratory who attests that it will be operated under CLIA, per 42 CFR 493.35(c)(2). The form's signature line is for the owner or director of the laboratory.

The CMS-116, Section by Section

Form CMS-116 is the application for every type of CLIA certificate: Waiver, Provider-Performed Microscopy, Compliance and Accreditation. The same form also handles changes, from a new director to a switch in certificate type. The current edition is dated 03/24 and carries OMB number 0938-0581, which expires March 31, 2027. CMS estimates it takes "one hour per response," and that is roughly right for a single waived site with its paperwork in order.

The form is short, but the instructions are strict: "INCOMPLETE APPLICATIONS CANNOT BE PROCESSED AND WILL BE RETURNED TO THE FACILITY." Most returns come from a handful of fields. Here is each section in order, with what the State Agency expects to see.

Which sections does each certificate type complete?

Section II tells you. A Certificate of Waiver applicant completes Sections I through VI and IX through X. A PPM applicant completes Sections I through VII and IX through X. Compliance and Accreditation applicants complete everything, I through X. Choose the certificate "based on the highest level of test complexity performed by your laboratory." If you need help deciding, start with the five CLIA certificate types.

How do you complete Sections I through V?

Section I: General information

Check the reason for filing: Initial Application (with an anticipated start date), Survey, Change in Certificate Type, Change in Laboratory Director, or Other Changes. Every change needs an effective date. A first-time applicant leaves the CLIA number blank; one is assigned when the application is processed.

Facility name. The instructions say to be specific, "particularly when it is a component of a larger entity," and warn that "the information provided is what will appear on your certificate." For a physician's office it may be the physician's name.
Federal tax identification number. The entity's EIN.
Email address. This is now the most important field on the form. The Quick Start Guide (March 2026) says "After March 1, 2026, CMS will send all fee coupons and CLIA certificates by email," and that mailing and corporate address fields "are no longer required." CMS recommends "a business email address that many laboratory staff access and use." Check the box to receive notifications and electronic certificates by email.
Facility address. The physical location where testing happens. It may include a floor or suite but "cannot be a Post Office box or Mail Stop."
Director name, phone and credentials. Required for every certificate type, including a waiver.

Use an inbox the lab controls. A personal address that leaves with an employee, or an outside vendor's address, is how fee coupons go missing. See email-only fee coupons and certificates.

Section II: Type of certificate requested

Check one box. If you choose Accreditation, also check the accreditation organization: The Joint Commission, ACHC, AABB, A2LA, CAP, COLA or ASHI. The form notes that you must provide "evidence of accreditation… or evidence of application for such accreditation within 11 months after receipt of your Certificate of Registration." A PPM or nonwaived applicant must also send proof of the director's qualifications with the form; the box below Section II says so in plain terms.

Section III: Type of laboratory

Pick the one code "most descriptive of the location where the laboratory testing is performed." There are 29 codes. The ones we see most:

21 Physician Office
20 Pharmacy
06 Community Clinic
09 Federally Qualified Health Center and 25 Rural Health Clinic
12 Home Health Agency and 13 Hospice
19 Mobile Laboratory (attach the vehicle identification numbers)
26 School/Student Health Service
22 Practitioner Other and 29 Other, each with a "specify" line

There is no separate code for urgent care or telehealth; those sites usually pick the code that matches who runs the testing location. Ask the State Agency if you are unsure.

Section IV: Hours of laboratory testing

List only the times testing actually happens, in HH:MM format, or check 24/7. The instructions say "Do not use military time."

Section V: Multiple sites

Section V is only for labs that qualify for one of the three regulatory exceptions to the one-certificate-per-location rule: a lab that moves from site to site (mobile units, health fairs, temporary locations), a not-for-profit or government lab doing limited public health testing (no more than a combination of 15 moderate complexity or waived tests per certificate), or hospital labs on one campus under common direction. Everyone else answers "No." A for-profit chain of clinics answers "No" and files one CMS-116 per location. See the multiple-site exception and mobile and temporary testing sites.

Where do the tests go in Sections VI through VIII?

Section VI: Waived testing

List "each analyte, test system, or device used in the laboratory": the analyte or test, the test name and the manufacturer. The form's example is a group A strep test with its product name and maker. Then give one estimated total annual volume for all waived tests. Build the list from each kit's package insert and confirm each test system's categorization in FDA's CLIA database, as described in how to tell whether a test is CLIA-waived. A vague entry such as "rapid tests" is a common reason for a call back from the State Agency.

Section VII: PPM testing

Check each of the nine provider-performed microscopy procedures you will perform, from wet mounts and KOH preparations to qualitative semen analysis, and give one annual volume. The form calls them "the only PPM tests that can be performed by a facility having a Certificate for PPM." More in the PPM certificate.

Section VIII: Nonwaived testing

Only Compliance and Accreditation applicants complete Section VIII. List each nonwaived test system with (M) for moderate or (H) for high complexity, check every specialty and subspecialty, and give an annual volume for each. The counting rules matter because volume and specialties set the fee schedule (42 CFR 493.638(c)):

Each non-calculated chemistry analyte counts separately, so a lipid panel of total cholesterol, HDL, LDL and triglycerides "equals 4 tests."
Do not count waived tests, calculations, quality control, quality assurance or proficiency testing.
A urinalysis dipstick counts as one test "regardless of the number of reagent pads on the strip," and it belongs in Section VI.

Who owns the lab, and which other labs does the director run?

Section IX: Type of control

Choose voluntary nonprofit, for profit (proprietary) or government, then answer a question added to the current edition: "Does this facility have partial or full ownership or control by a non-United States-based government or entity?" If yes, name the country.

Section X: Director affiliation with other laboratories

List every other separately certified lab this director directs, including Certificate of Waiver labs, by CLIA number and name. The instructions note that "for a Certificate for PPM, Certificate of Compliance or Certificate of Accreditation, an individual can only serve as the director for no more than five certificates." See the five-lab limit.

Who signs, and what does the signature mean?

The last page carries two things the signer is agreeing to. The first is a warning that anyone who intentionally violates CLIA "shall be imprisoned for not more than 1 year or fined," with up to 3 years for a repeat violation. The second is a consent that the laboratory "will be operated in accordance with applicable standards" and that the Secretary may "inspect the laboratory and its operations and its pertinent records at any reasonable time."

The regulation says the application must be "signed by an owner, or by an authorized representative of the laboratory" who makes that attestation (42 CFR 493.35(c)(2), with the same words at 493.43(c)(2) and 493.55(c)(2)). The form prints the director's and owner's names and has one line: "SIGNATURE OF OWNER/DIRECTOR OF LABORATORY (SIGN IN INK OR USE A SECURE ELECTRONIC SIGNATURE)." An outside preparer is not the owner or director and cannot give that consent, so the owner or director signs.

Where does the finished form go?

"Completed 116 applications must be sent to your local State Agency. Do not send any payment with your completed 116 application." CMS lists each state's CLIA office in its State Agency contact file; see your CLIA State Agency. Some states want a supplement with the CMS-116, such as Texas Form 3225 (Texas Form 3225 and CLIA in Texas). After processing, the lab receives an emailed fee coupon with its CLIA number and pays on pay.gov.

A short checklist before you send it:

Every applicable section complete, with no blank required fields.
A physical street address, not a P.O. box.
A shared business email the lab controls.
Each test listed by name and manufacturer, with an annual volume.
Director qualification documents attached for PPM, Compliance or Accreditation.
Signed and dated by the owner or director.
No check or payment enclosed.

Can someone prepare the CMS-116 for the lab?

Yes. Nothing in the form or the regulation stops a preparer from completing it, as long as the owner or director reviews the answers and signs. White Glove CLIA prepares the CMS-116 and the test menu, assembles the director documents for PPM and nonwaived filings, and can send the signed packet to the State Agency. The lab keeps its own email, pays CMS from its own coupon and pays any state fee directly. A Certificate of Waiver Application is $399 per site, a PPM Certificate Application is $599 per site, and a CLIA Change Request is $149 per change.