Physician Office Labs in New York

New York is exempt from federal CLIA, but not every New York lab is outside the federal program. The Wadsworth Center runs two programs, and which one a site uses depends on who owns it and whose patients it tests. A practice that qualifies as a physician office laboratory (POL) applies to the Physician Office Laboratory Evaluation Program (POLEP) on the federal CMS-116 and follows federal rules. Every other site goes to the Clinical Laboratory Evaluation Program (CLEP).

POLEP describes its role this way: it works "under contract with the Center for Medicare and Medicaid Services (CMS)" and "is responsible for managing activities related to administration of the federal program implementing the Clinical Laboratory Improvement Amendment of 1988 (CLIA) for physician office laboratories (POL) throughout New York." And: "POLEP follows Federal regulations only (§493), hence we accept the CMS-116 application."

Which practices count as a physician office lab?

The test comes from New York Public Health Law § 579(1). POLEP: "To meet the POL exception, the facility must be entirely owned and operated by medical professionals allowed in §579.1 and perform laboratory tests, personally or through their own employees, solely as an adjunct to the treatment of their own patients."

Three parts of that sentence decide most cases:

• Entirely owned and operated by practitioners the statute lists. A practice owned by a hospital, a management company or outside investors does not meet it. CLEP's own list of Limited Service Laboratories includes "hospital owned physician practices."
• Personally or through their own employees. Testing staff belong to the practice.
• Solely as an adjunct to the treatment of their own patients. A practice that accepts specimens from other practices is running a reference lab, not a POL.

POLEP's application page adds two structural limits. On the CMS-116, "The only type of laboratory accepted in this program is a physician office," and "POLs are Proprietary/For Profit. If the facility type does not meet this requirement, submit your application through the Clinical Laboratory Evaluation Program." A not-for-profit clinic, a pharmacy, a school health office or an urgent care center owned by outside investors does not file here; see New York's Limited Service Laboratory registration for that route.

What does POLEP require beyond the CMS-116?

POLEP's initial application page lists more than the federal form:

1. The CMS-116, with the facility name matching "the name of your business entity registered with the IRS for the facility's federal tax identification number." A doing-business-as name goes on the form too.
2. Disclosure of Ownership, Form DOH-5793.
3. An IRS letter showing the facility's name and tax ID, "commonly referred to as form SS-4."
4. The director's current New York license to practice, if applicable.
5. A management contract, or a statement that there is none. "Any laboratory that is operated and/or managed by an individual or entity on behalf of the owner must provide a copy of the written agreement."
6. Director qualification documents for any moderate or high complexity testing.

POLEP also asks that "All sections of the application must be filled out," with "NA" or "No" where an item does not apply, and estimated annual volumes for every waived test, PPM procedure and nonwaived specialty. It strongly recommends a fax number and email address on page 1. Since March 1, 2026, CMS sends fee coupons and certificates by email, so that address is how your bill arrives.

Does the multiple-site exception work for New York practices?

No. POLEP says Section V of the CMS-116, the multi-site exemption, "does not apply to POLs in New York State. You may only test patients of your medical practice for the purposes of treatment and diagnosis." Federal rules let mobile units and temporary testing sites share a home base's certificate; POLEP does not accept that for physician offices. A practice with offices in Manhattan and Westchester treats each office as its own lab. POLEP asks practices with questions about testing at different locations to contact the program at clia@health.ny.gov.

Who pays, and what?

A POL holds a federal certificate, so it pays the federal fee to CMS, not a state registration fee. As of October 2026 the CMS fee for a Certificate of Waiver is $248 for two years and for a PPM certificate $297. The lab pays from its own emailed coupon on pay.gov. POLEP adds one more note for anyone testing for COVID-19: "All positive (molecular and antigen) and negative molecular COVID results must be reported under federal CLIA regulation," which a facility can meet through the Department's Electronic Clinical Laboratory Reporting System.

How does a POL report changes?

POLEP splits changes into two groups. A new CMS-116 is required for a certificate type change, reinstatement, a specialty change, a change of accreditation organization, a director change for PPM, Compliance or Accreditation labs, and a change of ownership. For ownership, POLEP wants the CMS-116, the IRS SS-4 or LTR147C, the DOH-5793, and "a Bill of Sale indicating transfer of ownership from one entity to the other (even if both entities are owned/controlled by the same individual(s))."

Written notice or a CMS-116 covers a change of DBA name, physical address, phone, email, closure, or the director of a Certificate of Waiver lab. The letter needs the lab name, CLIA number, director's name, the change, and "Signature of the Laboratory Director with date of signature."

Ownership matters twice in New York. If a practice is sold to a hospital system or a corporate group, it may stop qualifying as a POL at all, and its testing then belongs under CLEP. Plan that move before the closing date, not after.

Where does our work fit?

We check whether your practice meets the POL test, prepare the CMS-116, the DOH-5793 and the test list from each kit's instructions, and list what your director needs to attach. The owner or director reviews and signs the form, and we can send the signed packet to POLEP. You pay CMS directly. A single office is $399 under our Certificate of Waiver Application, or $599 for a PPM certificate. The New York requirements page compares the POLEP and CLEP routes.