CLIA for Physician Offices

Physician office labs are the backbone of CLIA. CMS's September 2026 statistics count 116,814 physician office labs, 38.8 percent of all 301,284 registered labs. Of the 114,313 office labs outside the two CLIA-exempt states, 84,829 hold a Certificate of Waiver, 16,123 hold a PPM certificate, and the rest hold compliance or accreditation certificates for moderate and high complexity testing.

The rule that brings an office in is short. CLIA applies "even if only one or a few basic tests are performed, and even if you are not charging for testing" (Form CMS-116 instructions). A practice that dips urine, runs a pregnancy test or checks a fingerstick glucose for a patient's care is a laboratory and needs a certificate.

Which certificate does a physician office need?

Choose by "the highest level of test complexity performed by your laboratory" (CMS-116 instructions):

• Certificate of Waiver if every test is categorized as waived. The original federal list in 42 CFR 493.15(c) reads like an office supply order: dipstick urinalysis, fecal occult blood, visual ovulation and urine pregnancy tests, non-automated sedimentation rate, home-use glucose meters, spun microhematocrit and single-analyte hemoglobin. FDA has categorized many more test systems as waived since, from rapid strep kits to A1c analyzers. The current CMS fee, as of October 2026, is $248 every two years.
• PPM certificate if a physician or midlevel practitioner personally performs any of the nine microscopy procedures, such as wet mounts, KOH preps or urine sediment exams, "during the patient's visit" (42 CFR 493.19). PPM also covers waived tests. The current CMS fee is $297. See the PPM certificate.
• Registration, then Compliance or Accreditation if the office runs any moderate or high complexity test, such as a chemistry or hematology analyzer not categorized as waived. That brings personnel standards, proficiency testing and biennial surveys. See moving from a waiver to moderate complexity testing.

When in doubt about a specific kit, the FDA CLIA database settles it. "Any test that has not been categorized is considered high complexity by default," CMS says. Our post on telling whether a test is CLIA-waived shows how to search it.

Which CMS-116 fields matter most for an office?

A waiver applicant completes Sections I through VI and IX through X. The points that matter most for an office:

• Facility name. "For a physician's office, this may be the name of the physician," and "the information provided is what will appear on your certificate."
• Facility type. Code 21, Physician Office, in Section III.
• Director. Name, phone number and credentials. For a waiver there are no federal director qualifications; for PPM the director must be a physician, a midlevel practitioner authorized by the state to practice independently, or another practitioner the rule names (42 CFR 493.1357), and documents proving it go with the form.
• Email address. Since March 1, 2026, CMS emails all fee coupons and certificates. Use an address the practice controls.
• Waived test table. Every analyte, test name and manufacturer, and the estimated annual volume.
• Ownership type and director's other labs. Sections IX and X.

The owner or director signs at the end, under a consent to "permit the Secretary... to inspect the laboratory and its operations and its pertinent records at any reasonable time." The signed form goes to the State Agency, not CMS, and "Do not send any payment with your completed 116 application." Our CMS-116 guide walks through every section.

How do group practices with several offices file?

One certificate per office that tests. A waiver lab "must file a separate application for each laboratory location" (42 CFR 493.35(a)), and a physician-owned group fits none of the three exceptions for one certificate across sites. See one certificate per site.

Two group-practice details are easy to miss. First, a PPM physician may examine specimens from "a patient of a group medical practice of which the physician is a member or an employee" (493.19(b)(1)(i)), so a group's patients count as the physician's own for PPM purposes. Second, a PPM director may direct "no more than five laboratories" (493.1359(a)), and Section X of every CMS-116 lists the other labs that director runs. A group with seven PPM offices needs at least two qualified directors. See the five-lab limit.

Can two practices share one lab room?

They can share the space but not the certificate. CMS allows "Multiple laboratories" to "operate at the same physical location (e.g., same building or suite, as applicable) with separate CLIA numbers, as long as each laboratory can demonstrate that it is operating as a separate and distinct entity." If they share testing staff and equipment, "All records (e.g., quality control, procedure manuals, personnel competency) must be kept separate and distinct for each laboratory," and "The times of testing cannot overlap and cannot be simultaneous" (State Operations Manual, Chapter 6, section 6009). CMS adds that they "are not to be referred to as 'shared laboratories,'" and that cost-sharing and billing questions "are not CLIA quality and safety issues."

How do states treat physician office labs?

This is where offices in different states diverge. Some examples from the statutes and rules themselves:

• New York is CLIA-exempt, but physician office labs are the exception to the exception. Its Physician Office Laboratory Evaluation Program "follows Federal regulations only," and accepts the CMS-116, for a facility "entirely owned and operated by medical professionals" listed in Public Health Law 579 that tests "solely as an adjunct to the treatment of their own patients." A hospital-owned practice does not qualify. See physician office labs in New York.
• Pennsylvania exempts a practitioner's office from its permit only when it performs listed procedures, among them dipstick urinalysis, urine sediment, pregnancy tests, blood counts, sedimentation rate, Gram stain and pinworm and Trichomonas tests (28 Pa. Code 5.1). A practice running rapid strep or A1c is outside that list. See Pennsylvania's clinical laboratory permit.
• Kentucky exempts labs "operated by a licensed physician, or a group of licensed physicians, solely and exclusively in connection with the diagnosis and treatment of their own patients," but "if any referred work is received or performed," the full licensing law applies (KRS 333.040(2)). See Kentucky.
• Maine exempts physicians, physician associates, family nurse practitioners and group practices testing their own patients, except that "laboratories incorporated for the mutual use of physician or group practice owners are subject to all provisions" of the Act (22 M.R.S. 2013-A). See Maine's limited license.
• Maryland lets the director of a physician office lab doing only waived tests hold a letter of exception instead of a permit (COMAR 10.10.03.02). See Maryland's Letter of Exception.
• California requires every lab doing waived or PPM testing to register with the state (Bus. & Prof. Code 1265(a)(2)). See California's registration.

After approval, what keeps an office lab out of trouble?

1. Follow each kit's instructions exactly (42 CFR 493.15(e)(1)); a modified procedure turns a waived test into high complexity.
2. Do not start a nonwaived test until the certificate covers it; waiver and PPM labs must notify the State Agency first (493.39(a), 493.53(a)).
3. Report a new owner, name, address or director within 30 days.
4. Keep the email on file current, and pay only coupons that come from CMS. CMS warned labs on October 7, 2026 about third-party mailings "styled as bills or invoices." See look-alike CLIA invoices.
5. For PPM, document competency evaluations "at least semiannually during the first year" each person tests, then at least annually (493.1359(d)).

What does our service cost for a practice?

We prepare the CMS-116, build the test table from each kit's instructions, and prepare any state registration or permit; the practice's owner or director reviews and signs, and the practice pays CMS and the state directly. A Certificate of Waiver Application is $399 per office, or $549 with a compliance binder. A PPM Certificate Application is $599 per office. State registrations are $299 per state, and full state licenses or permits are $699. Payer enrollment of the CLIA number belongs to our sister company, White Glove Credentialing; its post on group practice credentialing covers that side.