All clinical and forensic laboratories and blood banks located in or accepting specimens from New York State must hold a New York State Department of Health clinical laboratory permit.

Detailed information about the Clinical Laboratory Evaluation Program can be found in the CLEP Program Guide_[1].

Laboratories applying for a New York State clinical laboratory permit may not begin testing on NYS specimens until all requirements have been met and a permit is issued. Clinical laboratory permits are valid for one year, commencing on July 1 of each year (initial permits can be issued at any time during the permit cycle of July 1 through June 30) and extending through June 30 of the following year.

Prior to applying for a permit, the laboratory director and any assistant directors must hold a Certificate of Qualification for all categories for which the laboratory offers testing to residents from New York State. Additional information is available on the Certificate of Qualification Application(s) website.

Applicants begin by submitting the following:

• A check in the amount of $1,100 payable to the New York State Department of Health for application and Inspection and Reference fees.
• Clinical Laboratory Permit Application_[2]
• Disclosure of Ownership, Controlling Interest, and Corporate Membership Statement_[3]
• Director Health Commerce System (HCS) Affiliation Request form_[4]

Please review all application materials for completeness prior to submission. Incomplete or incorrect applications, or failure to submit all required forms and application fees will result in delayed processing.

Supporting information:

• Laboratory Standards_[5]
• CLEP Program Guide_[6]
• Laws and Regulations_[7]
• 2023 - 2024 Permit Category Descriptions_[8]

Notes:

Names of the director, all assistant directors and the owner should be printed or typed clearly on the last page of the application or on a separate sheet if necessary. Corresponding signatures and dates must be included. Electronic signatures and signature stamps are not acceptable on any article enclosed in an application package.

Application fees: Total fees due at time of application are $1,100.00. This includes a non-refundable $100 application fee and a $1,000 Inspection and Reference fee. This is payable by check made out to the New York State Department of Health.  Credit card payments are not accepted. Checks drawn on banks located outside the United States are not accepted. Laboratories located outside the United States must contact CLEP at clep@health.ny.gov_[9] to determine an acceptable alternate payment method. 

Test Menu:  A Test Menu will be sent electronically once your application is reviewed. A Test Menu is required for all categories for which your laboratory performs testing on specimens from NYS. Categories of testing can be found in the Permit Category Descriptions document. Please be sure Test Menu has a corresponding category selected on pages 6 & 7 of your Clinical Laboratory Permit Application. Test menus should be submitted to clepcert@health.ny.gov_[10] and must include the Permanent Facility Identifier (PFI) number that will be assigned to your laboratory.  The laboratory director or an assistant director must be assigned responsibility for each category indicated on pages 6 & 7 of your Clinical Laboratory Permit Application.

Optional documents, as applicable to the laboratory:

• Certificate of Qualification Application_[11](s) for director and assistant directors (if individuals do not already hold Certificate)

• Copy of management contract

Please be advised that New York State Public Health Law stipulates that a laboratory permit is automatically void upon a change of director, owner or location. Proper and timely notification of these changes is required to stay this void.

CLIA Registration: Under our authority as a CLIA-Exempt State Program, laboratories located in New York State will be assigned a CLIA number by this office once the laboratory is placed in application for a permit. CLIA numbers will appear on your State laboratory permit and laboratories in New York State are not required to hold a separate CLIA certificate. If your laboratory is located in New York State and does not yet have a CLIA registration number, check the box marked “Requested” and a CLIA number will be issued for your facility. If you are a non-NYS laboratory that has applied directly to the CLIA program but have not yet received your CLIA Number, check "Pending.” If your laboratory is currently operating as a physician office laboratory (POL), provide your current CLIA registration number.

Certification: It is the responsibility of both the director and the owner to ensure that the laboratory meets all legal requirements for operation on the Laws and Regulations section of our website.

Notification of Laboratory Changes: Notification of changes in the laboratory name, owner, director, or location, and requests for new categories or analytes must be submitted, prior to the effective date of the change, via eCLEP. At a minimum, the laboratory director must have completed the HCS account creation process prior to submitting changes via eCLEP. Please call CLEP at (518) 485-5378 if changes must be made before the laboratory director has been granted access to HCS.

Out of State Laboratories:  Non-New York State corporations may not do business in New York State until they have been authorized to do so by the New York State Secretary of State. Applications for a Certificate of Authority to do business in New York State may be obtained from the Department of State, Division of Corporations, State Records and Uniform Commercial Code, 99 Washington Avenue, 6th floor, Albany, NY 12231. Refer to the Department of State website at www.dos.ny.gov_[12]. Questions regarding this requirement can be directed to the Division at (518) 473-2492.

Medicaid Enrollment: Refer to the webpage eMedNY for instructions on Medicaid enrollment for New York State. The eMedNY Call Center number is 1-800-343-9000.

Workers Compensation: Under the New York State Workers’ Compensation Law, businesses applying for permits or licenses issued by the State must hold workers’ compensation and disability benefits coverage or document their qualifying for an exemption. Information regarding this requirement and the process for submitting proof of enrollment can be found in the New York State Workers’ Compensation Board's Employers’ webpage_[13].

Patient Service Centers and Health Fairs: If your laboratory plans to operate PATIENT SERVICE CENTERS (collection stations), or HEALTH FAIRS (temporary off-site testing events), the laboratory must apply via eCLEP after the clinical laboratory permit has been issued.

Limited Service Laboratories: If your laboratory plans to operate a LIMITED SERVICE LABORATORY (usually extension clinics offering waived or provider-performed microscopy procedures), you must complete and return an “Application for Limited Service Laboratory” (form DOH-4081)_[14].

Management Contracts: 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 (management contract) setting up the business relationship.

Proficiency Testing: The laboratory must indicate the CMS-approved provider and survey module that has been determined to fulfill CMS proficiency testing requirements for tests/analytes included under CLIA Subpart I (CFR 493.909-493-959). See to the list of CMS-Approved providers_[15].  An acceptable module must be chosen for each analyte on the Test Menu form where proficiency testing is required.