NYSDOH CLEP LDT Compliance Consulting
Last updated: October 2026
A clinical laboratory located in, or accepting specimens from, New York State must hold a New York State Department of Health (NYSDOH) clinical laboratory permit, and a laboratory-developed test (LDT) used on New York specimens is reviewed through the Clinical Laboratory Evaluation Program (CLEP) at the Wadsworth Center (NYSDOH Wadsworth Center, Obtain a Permit, page opened October 4, 2026).
Integral Healthcare Solutions (IHS), founded in 2002 by Thomas G. Goddard, JD, PhD, former Chief Operating Officer and General Counsel of URAC, guides laboratories through the CLEP lifecycle: gap assessment, method validation documentation, application preparation, RFI response, on-site survey preparation and annual permit renewal. IHS drafts the SOPs, indexes the validation package and drafts RFI responses for your laboratory director to review and approve, and your organization's named contact submits to NYSDOH.
What is NYSDOH CLEP, and why does it matter for LDTs?
CLEP is the NYSDOH program that regulates clinical laboratory testing in New York State, and it has reviewed LDTs since 1991 (NYSDOH Wadsworth Center, CLEP LDT review data, page opened October 4, 2026). It is a mandatory state requirement, not a voluntary accreditation.
NYSDOH states that only laboratories holding a New York State clinical laboratory permit are authorized to test specimens originating from New York, that LDT review begins after the permit application is submitted and that LDT review is not offered as a stand-alone service (NYSDOH Wadsworth Center, Test Approval, page opened October 4, 2026).
NYSDOH published review data in November 2023. The program had received more than 15,000 LDT applications as of March 2020, and NYSDOH notes that figure counts modifications to approved LDTs and is not a count of unique tests. Of 2,665 LDTs received between January 1, 2018 and December 31, 2020, 77 percent came from facilities outside New York and 23 percent from New York, and the NYSDOH table also lists 0.2 percent from outside the United States (NYSDOH Wadsworth Center, CLEP LDT review data, page opened October 4, 2026).
Who must obtain a NYSDOH permit with CLEP-approved tests?
Any laboratory that tests specimens from New York, wherever the laboratory is located, must hold the permit. Common cases are listed below.
- Molecular and genomic diagnostic laboratories, including NGS panels. NYSDOH publishes submission checklists for germline and somatic NGS variant detection.
- Commercial reference laboratories with national operations that accept New York specimens.
- Clinical trial laboratories that test participant specimens for participant management, where results inform clinical decisions. NYSDOH describes a separate submission path for those LDTs.
- Hospital-at-home and novel delivery models. NYSDOH has stated that CLEP's authority applies wherever testing is performed, including at home (NYSDOH Wadsworth Center, Hospital-at-Home news, page opened October 4, 2026).
- Academic medical center laboratories developing new assays.
When does a laboratory not need CLEP approval?
A laboratory that never accepts New York specimens does not need CLEP approval. A laboratory looking for legal advice on whether a particular test needs approval should ask counsel and NYSDOH. IHS does not give legal opinions.
Does CAP accreditation or CLIA certification replace the New York permit?
NYSDOH lists what it requires before it issues a permit: Certificates of Qualification for the director and assistant directors, an on-site survey with deficiencies corrected, successful proficiency testing, test approval where applicable, a Health Commerce System account for the director and payment of all fees (NYSDOH Wadsworth Center, Obtain a Permit, page opened October 4, 2026). Accreditation by another body is not on that list, so IHS's reading is that a CAP-accredited laboratory still needs the permit and test approval.
How does the 2024 FDA LDT rule affect CLEP?
FDA's page on laboratory-developed tests states that on May 6, 2024 FDA issued a final rule amending the definition of in vitro diagnostic products, that a federal district court vacated that rule on March 31, 2025 and that on September 19, 2025 FDA issued a final rule reverting to the regulation's text as it stood before the May 2024 rule (FDA, Laboratory Developed Tests, page opened October 4, 2026). The New York requirement is a state requirement, so IHS's reading is that the federal vacatur does not change it.
What changed in the New York regulations in 2026?
NYSDOH states that Subpart 58-1 of Title 10 NYCRR was amended and new Subpart 58-6 was adopted on September 2, 2026. Subpart 58-6 replaces Part 19 and sets out two Certificates of Qualification for laboratory directorship, a Laboratory Director CQ and a Technical Director CQ (NYSDOH Wadsworth Center, Amended Regulations Adopted, page opened October 4, 2026).
NYSDOH's CQ page says a Laboratory Director CQ does not authorize oversight of specific permit categories, which needs a Technical Director CQ. It also says a Laboratory Director who does not meet the Subpart 58-6 requirements and holds a CQ expiring after September 2026 must be replaced by a qualified director by January 1, 2027 (NYSDOH Wadsworth Center, CQ Requirements and Transition Guidelines, page opened October 4, 2026).
How does NYSDOH classify LDTs by risk?
NYSDOH requires a Risk Attestation Form with every LDT submission and assigns a classification of high, moderate, low, clinical trial or lifestyle. It states that laboratories are notified of the risk assignment within three weeks of a complete package, and that it cannot make pre-submission risk determinations (NYSDOH Wadsworth Center, Test Approval, page opened October 4, 2026).
| Classification | What NYSDOH says |
|---|---|
| High | No conditional approval. Testing cannot be offered on New York specimens until review is complete and full approval is granted. Packages from laboratories pending a permit or permit category are assigned high risk unless they qualify as clinical trial or lifestyle. |
| Moderate | Conditional approval if the laboratory holds a permit in the right category. The laboratory may offer the test once notified, and NYSDOH may withhold or withdraw conditional approval. |
| Low | Full approval without review if the laboratory holds a permit in the right category, though NYSDOH reserves the right to require review. |
| Clinical trial | NYSDOH acknowledges the test as part of a clinical trial approved by the NIH or another independent IRB. |
| Lifestyle (not evaluated) | The test may be offered with a disclaimer that NYSDOH has not evaluated it. |
IHS prepares the Risk Attestation Form from your validation data so that it describes the test accurately. NYSDOH decides the classification.
What is the CLEP approval process, and how long does it take?
IHS plans for roughly 12 to 14 months from gap assessment to permit issuance for an initial applicant, and 6 to 9 months for an existing permit holder adding a test category. These are IHS planning ranges, not NYSDOH figures.
NYSDOH review data shows requests for additional information are common. For LDTs approved on or before September 30, 2021, 46 percent had no request for more information, 33 percent had one, 14 percent had two, 5 percent had three and 2 percent had more than three (NYSDOH Wadsworth Center, CLEP LDT review data, page opened October 4, 2026). NYSDOH states that a response to a request for additional information is due within 60 days, that extensions can be requested and that failure to respond inactivates the LDT approval request (Test Approval).
Step 0: Certificates of Qualification
Before applying, the laboratory director and any assistant directors must hold Certificates of Qualification for every category the laboratory offers to New York residents (Obtain a Permit). IHS cannot speed up CQ processing, so IHS plans 2-4 months for this step and starts it first.
Phase 1: Gap assessment (weeks 1-3, IHS planning range)
IHS reviews your SOPs, validation data, quality management documents and personnel records against NYSDOH's requirements, maps personnel CQ needs, and ranks every documentation gap.
Phase 2: Documentation build (months 1-4, IHS planning range)
IHS drafts SOPs for the pre-analytic, analytic and post-analytic processes, organizes method validation data against NYSDOH's category checklist and prepares the Risk Attestation Form. NYSDOH publishes checklists for cellular immunology, cytogenetics FISH, diagnostic immunology, forensic identity, molecular genetics, molecular microbiology, oncology molecular, toxicology and trace elements, and a general checklist for other categories. Scientific content, including bioinformatics for NGS tests, comes from your laboratory staff and director.
Phase 3: Application package (months 4-5, IHS planning range)
An initial application starts with the Clinical Laboratory Permit Application, the Disclosure of Ownership statement and a check for the application fees. NYSDOH sends a Test Menu form after it reviews the application, and the form must be returned with the laboratory's Permanent Facility Identifier (Obtain a Permit). IHS assembles and checks the package, and your named contact submits it.
Phase 4: Responding to requests for information
IHS drafts answers to NYSDOH's questions for your director to review and tracks the 60-day response date.
Phase 5: On-site survey
NYSDOH states that laboratories seeking a permit must have an initial on-site survey before a permit is issued, that out-of-state surveys are announced and that routine surveys of in-state laboratories are unannounced. The survey checks premises, laboratory practice, equipment, personnel and record-keeping, and it follows a Recreation of the Test Process tool that traces specific patient results through pre-analytic, analytic, personnel and post-analytic steps. Each survey requires a completed Facility Personnel Form (NYSDOH Wadsworth Center, On-Site Survey Process, page opened October 4, 2026). IHS prepares your staff for the walkthrough and the documentation review.
Phase 6: Permit issuance and renewal
NYSDOH issues a permit when the directors hold their CQs, the survey is done and deficiencies are corrected, proficiency testing is successful, test approval is granted, the director has a Health Commerce System account and all fees are paid. Permits run for one year starting July 1 (Obtain a Permit). Reapplication is annual through eCLEP, and the period for permit year 2026-2027 opened April 1, 2026 with submission due April 27, 2026 (NYSDOH Wadsworth Center, Re-Apply for a Permit, page opened October 4, 2026).
What does a NYSDOH CLEP permit cost?
The cost has three parts: NYSDOH fees, IHS consulting and your internal time. NYSDOH sets and publishes its own fees, and IHS sets a fixed fee for each engagement after a free discovery session, because scope, number of sites and gap severity change the work.
- Initial application: the NYSDOH permit page states total fees of $1,100 at application, made up of a non-refundable $100 application fee and a $1,000 Inspection and Reference fee, payable by check (NYSDOH Wadsworth Center, Obtain a Permit, page opened October 4, 2026). Verify current fees with the New York State Department of Health.
- Annual reapplication: the NYSDOH re-apply page states a $100 reapplication fee each year (Re-Apply for a Permit, page opened October 4, 2026). Verify current fees with the New York State Department of Health.
- Annual permit and reference fees: NYSDOH calculates each laboratory's fee by multiplying the program's operating expenses by the laboratory's share of gross annual receipts among all permitted laboratories. For a laboratory outside New York, reported receipts reflect testing of specimens collected in New York (NYSDOH Wadsworth Center, Laboratory Fees, page opened October 4, 2026).
- Survey travel: New York Public Health Law requires out-of-state laboratories seeking or reapplying for a permit to pay survey travel expenses, which depend on surveyor numbers, survey days and facilities surveyed (same fees page).
How does IHS help with NYSDOH CLEP compliance?
The IHS process covers standards acquisition, gap assessment, document and evidence mapping, mock review against NYSDOH's published requirements and readiness support. Dr. Goddard personally leads IHS's NYSDOH CLEP/LDT engagements. IHS delivers this work under its Compliance Services practice line.
- Out-of-state laboratories: IHS plans for the gross annual receipts reporting basis, survey travel and remote management of quality documents.
- NGS and genomics submissions: IHS maps your documents to NYSDOH's published NGS checklists, and your scientists supply the technical content.
What this is not
- IHS is not NYSDOH and does not grant, deny or influence a permit or test approval.
- IHS drafts, and your organization's named contact files with NYSDOH and answers its questions. IHS does not communicate with NYSDOH for you.
- IHS is not a law firm. This page is not legal advice and does not guarantee a permit or an approval.
Frequently asked questions
See our complete NYSDOH CLEP LDT Compliance FAQ for more questions.
Does my laboratory need a New York permit if it is located outside New York?
Yes, if it accepts specimens originating from New York. NYSDOH states that all clinical laboratories located in or accepting specimens from New York State must hold a NYSDOH clinical laboratory permit.
Does CAP accreditation satisfy the New York requirements?
NYSDOH's conditions for issuing a permit do not list accreditation by another body, so IHS's reading is that a CAP-accredited laboratory still needs the permit and test approval. Confirm your own case with NYSDOH.
How does the risk classification affect timing?
NYSDOH notifies you of the risk assignment within three weeks of a complete package. Low-risk tests receive full approval without review, moderate-risk tests receive conditional approval during review and high-risk tests cannot be offered until review is complete.
How long does CLEP approval take?
IHS plans 12 to 14 months for an initial applicant and 6 to 9 months to add a category, as IHS planning ranges. The NYSDOH pages IHS read give no single duration, and requests for additional information are common.
What does it cost?
NYSDOH's published application fees total $1,100 and the annual reapplication fee is $100 (pages opened October 4, 2026). Verify current fees with the New York State Department of Health. IHS sets a fixed fee for each engagement after a free discovery session.
What does the on-site survey examine?
NYSDOH states that it examines premises, laboratory practice, equipment, personnel and record-keeping, using a Recreation of the Test Process tool for sample patient results. Out-of-state surveys are announced.
What does an IHS engagement include?
IHS drafts SOPs, organizes the validation package and drafts responses to NYSDOH questions for your laboratory director to review and approve. Your organization's named contact submits to NYSDOH.
Who is this not for?
A laboratory that does not accept New York specimens, or one that wants legal advice or direct dealings with NYSDOH from IHS, is not a fit. IHS is not a law firm and does not communicate with NYSDOH for you.
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