Pennsylvania's Clinical Laboratory Permit

Pennsylvania is one of the states where a federal CLIA certificate is not enough. Its rule is short: "No person, organization or establishment may operate a clinical laboratory in this Commonwealth without first obtaining a permit from the Department" (28 Pa. Code § 5.11(a)). The Department of Health's Bureau of Laboratories issues the permit, and the Bureau is also Pennsylvania's CLIA State Agency, so the federal and state applications travel together.

The Bureau's Division of Laboratory Improvement says Pennsylvania's licensure laws "apply to Pennsylvania's over 9,000 clinical laboratories." Its permit checklist (revised October 2025) names the lab types that apply: "Hospital, Independent, Mobile, Nursing Home, Pharmacy, Physician Office/Clinic, Screening Sites, and State Health Centers."

Is a physician office exempt?

Only if it runs a narrow, decades-old list of tests. The definition of "clinical laboratory" in 28 Pa. Code § 5.1 includes labs "operated in private offices and clinics of practitioners of the healing arts," then excludes "the office or clinic of a licensed practitioner of the healing arts who performs only the following procedures as part of his or her examinations of the patient":

• chemical examinations of urine by "Dipstik" or tablet methods;
• microscopic examination of urine sediment;
• pregnancy tests;
• red and white blood cell counts;
• sedimentation rate of blood;
• Gram stain;
• primary culturing for transmittal to a licensed laboratory;
• qualitative chemical examination of stool specimens;
• test for pinworms; and
• test for Trichomonas vaginalis.

That list was last amended in 1976. Rapid strep, influenza and COVID-19 antigen tests, A1c, lipid panels and most other waived tests a modern practice runs are not on it. A practice that adds even one of them is a "clinical laboratory" under § 5.1 and needs a permit, Certificate of Waiver or not. The Bureau's own guidance, "Understanding Clinical Laboratory Regulations in Pennsylvania" (revised October 2025), lists "physician's office laboratory/clinic laboratory" among the labs the definition includes. It describes a physician's office laboratory as one that "performs clinical laboratory testing only on its own patients or those of the practice" and "does not receive specimens from other physicians' offices or laboratories." The same document confirms the line CLIA draws: "Facilities only collecting or preparing specimens (or both) and not performing testing are not considered laboratories."

What goes in a Pennsylvania application packet?

The Bureau's checklist treats the state permit and the CMS-116 as one packet sent to the Bureau of Laboratories in Exton:

1. The PA Clinical Laboratory Permit Application for In-State Laboratories, completed and signed. Labs running waived tests complete Appendix B, Waived Testing; mobile and screening locations add Appendix F; PPM labs add Appendix C.
2. The CMS-116, completed and signed.
3. Matching data. The checklist asks applicants to verify that the lab address, lab director name and federal tax ID are the same on both forms and that "both applications are signed by the Director and Owner."
4. Director documents. For a waiver lab directed by a physician, a copy of the medical license and proof of any board certifications; the checklist also asks every lab for proof of the director's doctoral degree.
5. A check or money order for $100 payable to the Pennsylvania Department of Health.

Appendix B, Waived Testing, is "To be completed by all labs that will perform waived tests. This includes any CLIA Certificate type." It is a checklist of waived tests by analyte, so the test list you submit must match the kits you will actually stock. Nonwaived versions of the same analytes, such as nonwaived influenza, RSV or SARS-CoV-2 kits, sit in a different appendix, and some of those carry proficiency testing requirements.

The permit application also carries two attestations. The owner or corporation certifies the application is true and correct. The director signs a separate Director's Attestation accepting "all directorship responsibilities for the Commonwealth of Pennsylvania purposes." The rule itself says the "Application for a permit to operate a clinical laboratory shall be made by the director" (§ 5.11(b)). The checklist asks applicants to "allow a minimum of 4 weeks for processing."

What does a waived lab's director promise?

More than federal CLIA asks. Under CLIA, a Certificate of Waiver lab has no director qualification rules. Pennsylvania's Director's Attestation includes this line: "I understand that as the director of a laboratory performing only waived testing, I am required to be continuously available virtually to the laboratory during all times when testing is performed, to provide telephone or electronic consultation as needed." Directors of nonwaived labs attest to on-site visits "once every 6 months, with at least 4 months between the minimum two on-site visits."

The Bureau's guidance document lists further requirements "for all laboratories": written procedures for every test (package inserts are acceptable), in-date materials used according to the manufacturer, quality control results recorded so they trace to patient results, and approved proficiency testing where the Bureau's instructions require it. Read the current Bureau guidance for how each applies to a waived-only site before you open.

How much does a permit cost, and when does it renew?

Section 5.11 sets two fees. A filing fee of $25 accompanies the application, and "an annual registration fee shall be paid in full to the Department" on or before August 15 each year "upon receipt of billing forms from the Department." That fee "shall be $100 for each category for which approval is granted," and "The maximum fee required for each laboratory will not exceed $500 per annum" (§ 5.11(h)). The categories are microbiology, hematology, clinical chemistry (including urinalysis), tissue pathology and radioisotope technics (§ 5.11(d)). The Bureau's current checklist asks for a $100 check with a new application.

Permits run on that August 15 cycle; the Bureau's Act 122 guidance says permits "are valid until August 15, 2015 and annually thereafter." From 2026, the Bureau says, "the Pennsylvania Clinical Laboratory Permit annual licensure invoices will be sent electronically." Those state invoices are separate from the CMS fee coupon for the federal certificate, which the lab also pays directly. As of October 2026 that federal fee is $248 every two years for a Certificate of Waiver.

Which changes need notice?

The Bureau's guidance: labs "Must notify the Bureau immediately of a change in director or location and within 30 days of a change in ownership, laboratory name or test menu." "Immediately" is stricter than the federal 30-day rule for directors. The Bureau publishes a Change of Status Form for these updates.

Do labs outside Pennsylvania need a permit too?

Yes, since Act 122 of 2013. The Bureau's Act 122 FAQ: "any person or clinical laboratory, either in-state or out-of-state, that tests specimens in the Commonwealth or collected within the Commonwealth must be licensed by the Department." Out-of-state labs use a separate application with a $100 fee. Its instructions add three details that trip up national labs: the director "must be a person who holds a doctorate level degree and who qualifies under Section 5.21" of the regulations, the director "must be the same for both State and CLIA purposes," and "Neither the state nor the federal government recognizes co-directors." The lab name "must be exactly the same as it appears on your CLIA certificate" and may be only 32 characters including spaces. Act 122 also bars labs from placing paid or unpaid staff in a practitioner's office to collect or process specimens. See testing specimens from other states.

Where do we come in?

We build the Pennsylvania packet: the permit application with the right appendices, the CMS-116, the test list from each kit's instructions, and a check that every field matches across both forms. Your director and owner review and sign the attestations; the fee checks come from your organization. We can send the signed packet to the Bureau for you. Our State Lab License or Permit service is $699 per state, alongside the $399 Certificate of Waiver Application, and Renewal and Compliance Tracking ($299 per year) watches the August 15 invoice and the change rules. The Pennsylvania requirements page keeps the details current.