Your CLIA State Agency: Where the CMS-116 Goes

CLIA is a federal program, but almost nobody applies to CMS directly. The CMS-116 instructions say "Completed 116 applications must be sent to your local State Agency," and CMS's Quick Start Guide (March 2026) lays out the path: the State Agency receives the form, CMS emails a fee coupon with the new CLIA number, the lab pays on pay.gov, and the certificate arrives by email. The State Agency is usually a unit of the state health department under contract with CMS. Knowing which office it is, and what it expects, is the first step of every new site.

How do you find your State Agency?

CMS publishes the list as "CLINICAL LABORATORY IMPROVEMENT AMENDMENTS (CLIA) STATE AGENCY CONTACTS," a PDF updated May 2026. Each entry gives the office name, mailing address, phone, fax and email. Use the copy on cms.gov rather than an address saved from an old application, because offices move and boxes change.

Some state pages and CMS's list do not agree on every detail. Texas's San Antonio regional phone number differs between the two. When they conflict, confirm with the office before you send anything.

Which states split the job, or hand it elsewhere?

• New York has two entries. "For Physician Office Laboratories in New York," the Physician Office Laboratory Evaluation Program (clia@health.ny.gov, (518) 485-5352). "For All Other Laboratory Facility Types in New York," the Clinical Laboratory Evaluation Program (clep@health.ny.gov, (518) 485-5378), which issues Limited Service Laboratory registrations and permits instead of taking a CMS-116. See New York's Limited Service Laboratory registration.
• Texas splits by region: Arlington, San Antonio, Houston, Tyler, and Austin, which includes West Texas. Each has its own email, and HHSC wants Form 3225 with every application. See Texas Form 3225.
• Washington has an entry but no CMS-116: "Please do not submit a Form CMS-116 for WA MTS Licensure." See Washington's Medical Test Site license.
• Vermont has no State Agency of its own. "Labs located in Vermont should contact the New Hampshire State Agency," the Health Facilities Administration in Concord (CLIA@dhhs.nh.gov).
• Territories. American Samoa and Guam, among others, are pointed to a CMS survey branch email rather than a local office.

Does the State Agency also issue a state license?

Sometimes the same office does both, and sometimes not. In Pennsylvania, the Bureau of Laboratories is the State Agency and also issues the state permit, so the two applications travel as one packet. In Hawaii, the Office of Health Care Assurance takes the CMS-116 and the Class I permit application. In California, Laboratory Field Services takes the CMS-116 and also handles the separate state registration. In Florida, AHCA remains the State Agency even though the state stopped licensing labs in 2018. Our overview of state lab licensing on top of CLIA explains which states add a license.

Which State Agencies have their own habits?

• Mail and original signatures. Virginia's Office of Licensure and Certification: "CLIA applications must be submitted by postal mail with an original director signature." Its page says applications "will be processed within 30 days of receipt."
• The director's signature. Iowa requires "the individual listed as the laboratory director to sign page 5 of the application." Kansas says all CLIA changes must be on a CMS-116 "signed by the laboratory director." North Carolina: "The 116 form must be signed by the laboratory director."
• Email. Kansas accepts applications by email or fax. Michigan says "The primary means of communication with Michigan CLIA State Agency will be via email" and that only one email address can be entered in the CMS database.
• Extra documents. DC Health wants a copy of the director's DC medical license, PhD or highest degree with the CMS-116, even for a waiver. See state forms filed with the CMS-116.

Federally, the application must "Be signed by an owner, or by an authorized representative of the laboratory" (42 CFR 493.35(c)(2)). Where the State Agency asks for the director, plan on the director. Nobody outside the lab can sign: the signature carries the lab's attestation that it will meet CLIA and its consent to inspection.

What never goes to the State Agency?

Money for the federal certificate. North Carolina: "No, do not send money to the state agency with your application." Florida: "CLIA fees should never be sent to the State of Florida." Texas: "Do not send payment for CLIA fees to HHSC." The State Agency enters the application; CMS bills the lab by emailed coupon, and the lab pays CMS on pay.gov. As of October 2026, the CMS fee for a Certificate of Waiver is $248 every two years.

That matters more since CMS's October 7, 2026 special alert on third-party mailings "styled as bills or invoices." CMS: "Official CLIA communications come only from CMS or your State Survey Agency." If something asks you to pay a CLIA fee to anyone else, check it against your State Agency and CMS before paying. See look-alike CLIA invoices.

After approval, what does the State Agency handle?

It handles changes. Director, name, address and ownership changes go to the State Agency on a CMS-116 or, in some states, by letter. Texas, for example, accepts many waiver-lab changes by letter signed by the lab director or designee, while ownership changes need a full new CMS-116. Federal rules give 30 days for most changes and require notice before a waiver lab tests outside its certificate. For Compliance labs, State Agency surveyors also carry out the inspections. A waiver lab is "Not routinely surveyed," the Quick Start Guide says, but HHS may inspect one, for example to evaluate complaints from the public (42 CFR 493.35(d)).

Can we deal with the State Agency for you?

We prepare the CMS-116 and whatever the State Agency adds for that state, and we can send the signed application to it, by mail where the state requires originals. Your owner or director signs; the CMS coupon goes to your own email for your team to pay. A single site is $399 under our Certificate of Waiver Application, and a CLIA Change Request is $149 per change.