New York Lab Consultant: CLEP Permits, CQ and CLIA Compliance

What is the New York Clinical Laboratory Evaluation Program (CLEP)?

CLEP is the NYSDOH Wadsworth Center program that oversees clinical laboratory testing in New York State. Its authority comes from Article 5, Title V of the New York Public Health Law. CLEP issues clinical laboratory permits and Certificates of Qualification, runs on-site surveys, monitors proficiency testing, and reviews laboratory developed tests (LDTs). According to CLEP, it is currently the only regulatory agency in the United States that formally reviews LDTs.

Is New York a CLIA-exempt state?

Yes, partially. CMS lists two CLIA-exempt states: Washington and New York. New York's exemption is partial. Labs located in New York that hold a valid CLEP permit are CLIA-exempt for all specialties and subspecialties, and CLEP assigns their CLIA number. Physician office laboratories are handled separately through New York's Physician Office Laboratory Evaluation Program (POLEP) and must get CLIA certification there.

Do out-of-state labs need a New York permit to test New York specimens?

Yes. CLEP requires a NYSDOH clinical laboratory permit for every clinical and forensic laboratory and blood bank located in New York State or accepting specimens from it. Only permit holders may test specimens that originate in New York. Out-of-state labs are surveyed on announced visits, pay the surveyors' travel expenses, and must be authorized by the NY Secretary of State to do business in New York.

How do you apply for a New York clinical laboratory permit?

You submit a Clinical Laboratory Permit Application, a Disclosure of Ownership statement, and a $1,100 check: a $100 non-refundable application fee plus a $1,000 inspection and reference fee. CLEP then sends a test menu. Before you apply, the director must already hold a CQ. You cannot test NY specimens until the permit is issued. Permits run from July 1 to June 30.

CLEP issues the permit once all of the following are true:

• The director (and any assistant or technical directors) holds CQs for every relevant category.

• The lab has passed an on-site survey and corrected any deficiencies.

• The lab has passed proficiency testing for each category and has authorized its PT provider to release results to New York.

• Test approval has been received, where it applies.

• The laboratory director has a Health Commerce System (HCS) account linked to the lab.

• All fees have been paid.

A permit is automatically void when the lab changes its director, owner or location. To keep it valid, notify CLEP through eCLEP before the change takes effect.

What is a Certificate of Qualification (CQ) for a New York laboratory director?

A CQ is the NYSDOH credential that New York Public Health Law requires of anyone named as director of a clinical laboratory or blood bank that holds or is applying for a NY permit. Under Subparts 58-1 and 58-6 of 10 NYCRR there are two types. A Laboratory Director CQ covers the role of laboratory director. A Technical Director CQ is needed to oversee specific permit categories.

How does someone apply for a New York Laboratory Director CQ?

The applicant must be a licensed physician or hold an earned doctorate with certification from a board listed in 10 NYCRR 58-6.2(d). The application needs:

• The completed form with an original signature

• A non-refundable $150 fee

• A current CV that lists publications

• Board certificates and any professional licenses

• Doctoral transcripts or a credential equivalency evaluation

Doctoral-degree holders, and physicians who are not board-certified in pathology, also need:

• A third-party letter documenting two years of directing or supervising high-complexity testing

• Proof of 20 credit hours in clinical laboratory operations

The applicant must also show training or experience from the last ten years. Legacy CQ holders who do not meet Subpart 58-6 must be replaced by a qualified director by January 1, 2027.

Can Sound Lab Consultants provide a New York CQ lab director?

Yes. Sound Lab Consultants offers New York CQ laboratory director services to labs that need a director holding a Certificate of Qualification for their NYSDOH permit. Each director arrangement is matched to the lab's permit categories and CQ requirements. Sound Lab Consultants also helps prepare the permit application, the personnel documents and the survey readiness work that go with it. Plans start at $500.

What happens during a CLEP on-site survey?

Every lab needs an on-site survey to get and keep a NY permit. Surveyors check the premises, practices, equipment, personnel and records against Public Health Law Article 5 Title V, 10 NYCRR Parts 19, 58, 63 and 70, and the NYS Clinical Laboratory Standards of Practice. Surveys include a "Recreation of the Test Process" that traces specific patient results from start to finish. Routine surveys of in-state labs are unannounced.

What is a Limited Service Laboratory in New York?

Facilities that perform only CLIA-waived tests and/or provider-performed microscopy procedures (PPMP) don't need a full permit. Instead, they register as a Limited Service Laboratory using form DOH-4081 and a $200 fee. Registrations last two years. The director must be a licensed practitioner or a PhD/DSc who holds a CQ, but PhD/DSc directors may not oversee PPMP sites. Independent physician-office labs testing their own patients go through POLEP instead.

New York permit preparation checklist

• ☐ Confirm which NYSDOH permit categories cover your test menu (2026-2027 Permit Category Descriptions)

• ☐ Confirm the laboratory director holds a Laboratory Director CQ and each category has a Technical Director CQ holder

• ☐ Complete the Clinical Laboratory Permit Application and Disclosure of Ownership statement, with original signatures

• ☐ Prepare the $1,100 check payable to the New York State Department of Health

• ☐ Out-of-state labs: get a Certificate of Authority from the NY Department of State

• ☐ Enroll in CMS-approved proficiency testing for each analyte and authorize the release of results to New York

• ☐ Prepare validation packages for LDTs and modified tests, following CLEP submission guidelines

• ☐ Set up the laboratory director's Health Commerce System (HCS) account and link it to the lab

• ☐ Have workers' compensation and disability coverage documentation ready

• ☐ Align SOPs, QC, IQCP and records with the NYS Clinical Laboratory Standards of Practice

• ☐ Run a mock "Recreation of the Test Process" on sample patient reports before the survey

• ☐ Provide a copy of any management contract, if someone else operates the lab

• ☐ Plan for eCLEP change notifications (director, owner, location, new categories) before they take effect

How Sound Lab Consultants helps

Sound Lab Consultants is a nationwide CLIA, CAP and COLA lab compliance consultant. For New York, Sound Lab Consultants helps labs with:

• NY CQ laboratory director services: directors who hold a Certificate of Qualification for labs that need one for their NYSDOH permit

• Permit application preparation: the application, ownership disclosure, test menu and category alignment

• CLEP readiness and gap reviews against the NYS Clinical Laboratory Standards of Practice

• SOP and QMS documentation, including document control, QC plans and audit roadmaps

• IQCP documentation for the CLIA, CAP and COLA programs that require it

• Validation documentation for test and device setup, LDTs and method verifications

• CLIA, CAP and COLA readiness for labs that also hold or are seeking those certifications

Plans start at $500.

Frequently asked questions

What does a New York lab consultant do?

A New York lab consultant helps clinical labs meet NYSDOH CLEP requirements. That includes preparing the permit application, meeting Certificate of Qualification director requirements, getting ready for the on-site survey, and maintaining quality documentation, along with CLIA, CAP and COLA compliance.

Does my out-of-state lab need a New York permit?

Yes, if it accepts specimens from New York. CLEP requires a NYSDOH clinical laboratory permit for any lab that is located in New York or accepts specimens from New York.

Do New York labs need a separate CLIA certificate?

Generally no. A New York lab that holds a CLEP permit is CLIA-exempt, and CLEP assigns its CLIA number. Physician office labs are the exception and get CLIA certification through POLEP.

How much does a New York clinical laboratory permit application cost?

$1,100 at the time of application: a $100 non-refundable application fee plus a $1,000 inspection and reference fee, paid by check to the New York State Department of Health. Out-of-state labs also pay the surveyors' travel expenses.

Who can be a laboratory director in New York?

Someone who holds a NYSDOH Laboratory Director CQ. That means a licensed physician, or an earned doctorate holder certified by a board listed in 10 NYCRR 58-6.2(d), with documented recent high-complexity experience. A Technical Director CQ is required for each permit category.

Can Sound Lab Consultants provide a CQ laboratory director for a New York permit?

Yes. Sound Lab Consultants offers New York CQ laboratory director services and also helps with the permit application and survey readiness. Plans start at $500.

How long is a New York lab permit valid?

Permits cover the cycle from July 1 to June 30. Initial permits can be issued at any point during the cycle. A permit is automatically void if the lab changes its director, owner or location without proper notice.

Do labs doing only waived testing need a full permit?

No. Facilities that perform only waived tests and/or PPMP register as a Limited Service Laboratory with form DOH-4081 and a $200 fee. The registration lasts two years.

Related pages: CLIA consultant · Laboratory director services · CAP laboratory consultant · COLA laboratory consultant · Clinical lab setup checklist · CLIA personnel rule changes 2024

Get help with your New York lab permit

Sound Lab Consultants helps labs prepare for CLEP permits, meet CQ director requirements, and stay compliant with CLIA, CAP and COLA. Plans start at $500.

Sound Lab Consultants · PO Box 2135, Chandler, AZ 85244