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Clinical Laboratory Services

About CLIA

What is CLIA?

The Clinical Laboratory Improvement Amendments of 1988 (CLIA) is a federal program under the jurisdiction of the Centers for Medicare and Medicaid Services (CMS). The CLIA amendments established quality standards for all laboratory testing to ensure the accuracy, reliability, and timeliness of patient test results regardless of where the test was performed.

On behalf of CMS, the Bureau of Survey and Certification (BSC) serves as the Michigan State Agency (SA) for federally certified programs participating with Medicare. Within BSC, the Laboratory Improvement Section manages the CLIA program and administers the certification of clinical laboratories in accordance with CLIA regulations.

CLIA program duties/activities include performing onsite inspections (referred to as surveys by CMS), ensuring accuracy and reliability of laboratory testing via proficiency testing review, investigating complaints, and monitoring approximately 10,000 clinical laboratories in Michigan.

The CLIA program is regulated for compliance under guidelines set forth in Federal Regulations 42 CFR Parts §493.1 through §493.1850.

Who needs a CLIA Certificate?

Any facility or provider that performs laboratory tests on human specimens for the purpose of diagnosis and/or treatment of disease is required by federal law to have a CLIA certificate. A CLIA certificate is required regardless of reimbursement and there is no minimum test volume. Plainly stated, a CLIA certificate must be obtained if only one test is performed, even if payment is not received.

A CLIA certificate IS NOT required for:

  • Blood draws
  • Specimen collections
  • Pre-employment drug/alcohol testing
  • Court ordered drug/alcohol testing
  • Breath alcohol testing
  • Forensic Testing
  • TB Skin Testing

Certificate Types

Certificate of Waiver

A Certificate of Waiver allows a facility to perform only tests that are categorized as waived by the Food and Drug Administration (FDA). As defined by CLIA, waived tests are “simple laboratory examinations and procedures that have an insignificant risk of an erroneous result.” Examples of waived tests include dipstick urinalysis, fecal occult blood, urine pregnancy tests, and blood glucose monitoring. The FDA maintains an online database of FDA approved laboratory testing and their respective categorization at the following link: FDA CLIA database

The main requirements for facilities performing waived testing are to follow the manufacturer’s instructions and to have a current CLIA certificate. There are no qualification requirements for the laboratory director or testing personnel of facilities/providers with a Certificate of Waiver.

A Certificate of Waiver also allows a facility to perform testing granted Emergency Use Authorization (EUA) by the FDA for use in a waived setting. EUA is usually associated with COVID-19 testing. The FDA maintains an online database of all testing granted EUA at the following link: In Vitro Diagnostics EUAs | FDA

Certificate for Provider Performed Microscopy Procedures (PPM)

The Certificate for Provider Performed Microscopy Procedures (PPM) is issued to facilities/providers that perform a limited list of tests requiring a microscope. A laboratory with this certificate may perform all CLIA waived tests and 9 approved microscopic procedures. PPM tests are considered moderately complex; therefore, the facility must comply with CLIA regulations for moderate complexity testing. The 9 approved microscopic procedures are listed on the CMS 116 application in Section VII. PPM Testing.

The director of a PPM laboratory must be a state licensed physician, midlevel practitioner, or dentist. When applying for a PPM certificate, the facility must provide a copy of the director’s current MI medical license, nursing license or dental license.

Certificate of Registration

The Certificate of Registration is initially issued to a laboratory that has applied for a Certificate of Compliance or a Certificate of Accreditation. This certificate permits the laboratory to perform moderate and/or high complexity laboratory testing until the survey is performed and the laboratory is found in compliance with the CLIA regulations.

Surveys for Certificate of Registration laboratories are generally conducted between 90 days and 12 months after the effective date of the certificate. Once the survey has been completed and the facility is found in compliance, the facility will receive a user fee coupon to obtain a Certificate of Compliance or a Certificate of Accreditation.

In addition to moderate and/or high complexity testing, a facility issued a Certificate of Registration can also perform PPM and waived testing.

Certificate of Compliance

A Certificate of Compliance allows a facility to conduct moderate and/or high complexity testing. This certificate is issued to a laboratory after a survey has been conducted and the facility is found in compliance with all applicable CLIA requirements.

Surveys for Certificate of Compliance laboratories are conducted by Michigan Department of Licensing and Regulatory Affairs laboratory evaluation specialists. Surveys for recertification of laboratories are conducted 6 – 12 months prior to the expiration date of the certificate.

The laboratory director of a Certificate of Compliance laboratory must be qualified to oversee non-waived testing. When applying for a Compliance certificate, or when changing the laboratory director, the facility must also submit documentation of the director’s qualifications.

In addition to moderate and high complexity testing, a facility that is issued a Certificate of Compliance can perform PPM and waived testing.

Certificate of Accreditation

A Certificate of Accreditation allows a facility to conduct moderate and/or high complexity testing. This certificate is issued to a laboratory after a survey has been conducted and the facility is found in compliance with all condition level CLIA requirements and Accrediting Organizations (AO) standards.

Surveys for Certificate of Accreditation laboratories are conducted by inspectors from the accreditation organizations.

The director of a facility with a Certificate of Accreditation must be qualified to oversee non-waived testing. When applying for an Accreditation Certificate, or when changing the laboratory director, the facility must also submit documentation of the director’s qualifications. Also, during the initial application process, the facility must select a specific Accreditation Organization(AO) on the CLIA application and provide evidence of enrollment with the organization.

In addition to moderate and high complexity testing, a facility that is issued a Certificate of Accreditation can perform PPM and waived testing.

Fees and Payments

CLIA Fees

**Effective 1/27/24, CMS implemented new fees for surveys and a fee increase for all certificate types**

CMS is responsible for all fees for CLIA certification. PAYMENT FOR CLIA FEES SHOULD NEVER BE SENT TO THE STATE OF MICHIGAN.

CMS will automatically generate a fee coupon when initial applications are processed and when an existing certificate is due to be renewed. Upon receipt of the fee coupon, follow the instructions provided on how to make payment. Payments may be submitted by US Mail or electronically, see Payment section for details. CLIA payments sent via US Mail should be submitted with the fee coupon. If you do not have a copy of the fee coupon, please include the CLIA ID number on the check or money order. Checks/money orders should be made payable to CLIA LABORATORY PROGRAM and mailed to the following address:

CLIA LABORATORY PROGRAM
PO BOX 3056
Portland, OR 97208-3056

CMS will send a total of 2 fee coupons - an initial fee coupon, then a rebill fee coupon 120 days later. Renewal certificates are mailed approximately 1-2 weeks before the current certificate expires.

If payment is not received prior to the expiration date, the certificate will be automatically terminated. A certificate can be reactivated if it has expired, please see Changes/Renewal section.

Fee Schedule

Certificate of Waiver
The fee for a Certificate of Waiver is $248. The certificate is valid for two years. Renewal fee coupons are mailed six months prior to the expiration date of the current certificate.

Certificate of Provider Performed Microscopy Procedures (PPMP)
The fee for a Provider Performed Microscopy Procedures Certificate (PPMP) is $297. The certificate is valid for two years. Renewal fee coupons are mailed six months prior to the expiration date of the current certificate.

Certificate of Compliance
There are 3 separate fees associated with a Certificate of Compliance:

  • Registration Fee. The Registration Fee is a one-time fee of $123 assessed to a laboratory that is initially applying for or changing their existing certificate to a Certificate of Compliance. It is valid for two years during which time a survey will be conducted to determine the laboratory’s actual annual test volume amount and regulatory compliance. A Certificate Fee will then be assessed, and, upon receipt of payment, the Certificate of Compliance will be issued to the laboratory.

     

  • Survey Fee. The Compliance Survey Fee is generated 12 months prior to the current certificate’s expiration date. This fee is assessed for the biennial survey that is conducted.

     

  • Certificate Fee. Once the survey is completed and the laboratory is recommended for recertification, the laboratory is issued a Compliance Certificate fee. This fee is assessed to pay for the renewed certificate. The amount of the fee may fluctuate due to changes in the laboratory’s annual test volume and number of laboratory specialties performed.

For a Certificate of Compliance please DO NOT estimate your fees. CMS will calculate the fee amount based on the annual testing volume and number of laboratory specialties performed and generate a user fee coupon for the correct amount.

Certificate of Accreditation
There are 3 separate fees associated with a Certificate of Accreditation:

  • Registration Fee. The Registration Fee is a one-time fee of $123 assessed to a laboratory that is initially applying for or changing their existing certificate to a Certificate of Accreditation. It is valid for two years during which time a survey by the accrediting agency will be conducted to determine the laboratory’s actual annual test volume amount and regulatory compliance.

     

  • Validation Fee. The Validation Survey Fee is generated 6 months prior to the current certificate’s expiration date. This fee must be paid to CMS every two years in addition to fees paid to the accrediting agency.

     

  • Certificate Fee. The Accreditation Certificate Fee is billed at the same time as the Validation Fee. This fee is assessed to pay for the renewed certificate. The amount of the fee may fluctuate biennially due to changes in the laboratory’s annual test volume and number of laboratory specialties performed. This fee must be paid to CMS every two years in addition to fees paid to the accrediting agency.

Additional Survey Fees

Rule CMS-332 implemented on 1/27/24 established new fees for the following CLIA program activities:

  •        On-Site Revisit Surveys
  •        Substantiated Complaint Surveys
  •        Proficiency Testing (PT) Desk Review Surveys
  •        Add-On Specialty Surveys

CMS will calculate the laboratory’s fee to cover the costs of these activities. The fee is based on resources and time necessary to perform the tasks.

CMS will revoke the laboratory’s certificate for failure to pay the assessed fees.

For more information, refer to the Federal Register on Register site. Please use search term: CMS-3326-F.

Payment

US Mail to the PO Box. Payment made by check or money order should be made payable to CLIA LABORATORY PROGRAM and mailed to:

CLIA LABORATORY PROGRAM
PO BOX 3056
Portland, OR 97208-3056

Fee coupons should be submitted with the check or money order. To ensure payments are applied to the correct laboratory, always write the CLIA ID number on the check or money order.

Online payment by credit card. Facilities that wish to make a payment by credit card can do so online through the Pay.gov website. Instructions to guide you through the process can be found HERE.

Complaints

How To File a Complaint

Complaints against a clinical laboratory or allegations of non-compliance with CLIA regulations may be made verbally or in writing and anonymously. 

A complaint may be filed using one of the following methods:

  1. Submit a complaint electronically via an online form at the following link: Health Facility Complaint Web Form 
  2. Complete a Health Facility Complaint Form (BCHS-361) and submit by mail, fax, or email
  3. Call the toll-free Complaint Hotline at (800) 882-6006

Complaint Intake Unit Contact Information

Department of Licensing & Regulatory Affairs
Bureau of Survey and Certification - Health Facility Complaints
PO Box 30838
Lansing, MI 48909

Phone: (800) 882-6006 
Email: LARA-BSC-Complaints@michigan.gov

Multiple/Temporary Sites & Out of State Testing/SampleCollection

Multiple Sites & Temporary Testing Sites

In general, the CLIA regulations require that a laboratory performing testing apply for a certificate for each laboratory location. The regulations do permit the following three exceptions:

1. Laboratories that are not at a fixed location, that is, laboratories that move from testing site to testing site, such as mobile units providing laboratory testing, health screening fairs, or other temporary testing locations may be covered under the certificate of the designated primary site or home base, using its address.

2. Not-for-profit or federal, state, or local government laboratories that engage in limited (not more than a combination of 15 moderately complex or waived tests per certificate) public health testing may file a single application.

3. Laboratories within a hospital that are located at contiguous buildings on the same campus and under common direction may file a single application or multiple applications for the laboratory sites within the same physical location or street address.

Facilities that qualify may submit their request on the CMS 116 application, see Section V. Multiple Sites. The laboratory should check “Yes” to the question “Are you applying for a single site CLIA certificate to cover multiple testing locations” and indicate which exception applies. Only one exception may be selected. The laboratory should fill out the bottom section indicating the name, address, and telephone number of each location and the tests performed. If additional space is needed, a separate sheet can be attached using the same format.

Please review CMS policy letter S&C: 12-09-CLIA explaining the CLIA multiple site exceptions.

 

Notification Requirements

Laboratories are required to submit written notification to the Michigan State Agency CLIA program of any change in multiple site status and when changes occur to the number or location of temporary testing sites. CMS memorandum QSO-22-13-CLIA outlines notification requirements for laboratories operating temporary testing sites. Written notification must include:

  • Laboratory name
  • CLIA number
  • Name of laboratory director AND owner
  • The change(s) being made – old information, new information, and effective date of the change
  • Signature of the laboratory director or their designee (someone with the authority to make changes)

In lieu of written notification, a new form CMS 116 CLIA Application is also acceptable. The CMS 116 application must be completed in its entirety.

Written notification or a CMS 116 application may be emailed to LARA-BSC-CLIA@michigan.gov or faxed to (517) 763-0214.

 

Out of State Testing & Sample Collection

Frequently the Michigan CLIA State Agency receives questions regarding testing in Michigan with a CLIA certificate issued from another state and/or what state licenses are needed regarding collecting patient samples from Michigan residents that will be processed in another state. Below are examples with responses that address the most asked questions.

We have an active CLIA in another state, do we have to apply for an out of state CLIA license to accept, collect, and process those patient samples in our laboratory? No. There are no licenses/approvals needed to accept, collect, or process patient samples from Michigan residents in an out of state laboratory. The receiving laboratory must be CLIA certified in accordance with federal law.

We have a CLIA license in another state. Can we cross state lines for Mobile Laboratory Testing using our current CLIA from the other state? Yes, but only if the CLIA certificate has requested a multiple site exception. Contact the CLIA State Agency where the CLIA certificate was issued to request a multiple site exception.

If we can use our current CLIA for mobile laboratory testing, is it limited to waived testing or is moderate complex testing allowed as well? The laboratory may perform all testing permitted under their certificate type. If performing non-waived testing, the laboratory needs to consider the following:

  • When mobile laboratory or temporary testing site equipment is not in use (weekends, overnight) how are instruments, reagents, stains, and other solutions protected from extreme temperature fluctuations? (Interpretive Guidance (IG), page 174)
  • Has the laboratory evaluated potential failures and sources of error due to the transport of instruments and reagents in a mobile laboratory? (IGs, page 205)
  • If equipment and reagents are used in mobile or temporary testing sites, how are they protected from extreme temperature fluctuations when not in use (e.g., evenings, weekends, and holidays)? (IGs, page 244)

Forms/Resources

Fillable Forms

CLIA application form, CMS-116  – The official form issued by the Centers for Medicare & Medicaid Services (CMS) to apply for a CLIA certificate.

CMS-209 Laboratory Personnel Report Form – The official form issued by the Centers for Medicare & Medicaid to list all laboratory personnel involved with moderate and/or highly complex testing.

CLIA Annual Test Menu Form – Form issued by the Michigan CLIA State Agency (SA) to list all tests performed by the laboratory. Tests sent out to a reference laboratory should not be included.

 

Payment Instructions

Online CLIA Payment – Instructions on how to use the Pay.gov system to pay CLIA fees online.

 

CLIA Brochures

CMS created brochures to help explain CLIA regulation requirements.

Brochure - How to Obtain a CLIA Certificate
This brochure explains when a CLIA certificate is required and how to obtain one.

Brochure - How to Obtain a CLIA Certificate of Waiver
This brochure explains when a CLIA certificate of Waiver is required and how to obtain one.

Brochure - Laboratory Director Responsibilities
What are your responsibilities as a laboratory director? This brochure explains the role and responsibilities of the laboratory director.

Brochure - What Do I Need to Do to Assess Personnel Competency?
This brochure explains the requirements for assessing the competency for laboratory personnel.

Brochure - Proficiency Testing
This brochure examines the DOs and DON’Ts of proficiency testing.

Brochure - Verification of Performance Specifications
This brochure provides information to assist your laboratory in meeting the CLIA requirement for verifying the performance specifications of unmodified, moderate complexity tests cleared or approved by the FDA.

Brochure - Calibration and Calibration Verification
This brochure provides information to assist your laboratory in meeting the CLIA requirement of calibration and calibration verification for all nonwaived (moderate and high complexity) test systems.

Brochure - Complaints, Do You Have a Concern About a Laboratory's Operation?
This brochure explains what to do if you have a complaint about a laboratory’s operation.

Brochure - CLIA IQCP, What is an IQCP?
This brochure provides a framework for customizing a quality control program for your test systems and your laboratory’s unique environment.

Brochure - CLIA IQCP, Considerations When Deciding to Develop an IQCP
This brochure provides information on what you need to know when developing an Individualized Quality Control Plan.

Brochure - CLIA Program and Medicare Laboratory Services
This brochure provides an overview of the Clinical Laboratory Improvement Amendments (CLIA) program.

 

Booklets

Provider Performed Microscopy Procedures – A Focus on Quality Practices
This booklet describes recommended practices for physicians, midlevel practitioners (nurse midwife, nurse practitioner, or physician assistant), and dentists who perform patient testing under a CLIA Certificate for PPM procedures. The booklet contains an overview of the regulatory requirements, resources including forms and examples, and an overview with images of common microscopic findings for the nine specific microscopic examinations that may be performed under a Certificate of PPM Procedures.

Ready? Set? Test! Booklet
This booklet describes recommended practices for physicians, nurses, medical assistants, pharmacists, and others who perform patient testing under a CLIA Certificate of Waiver. The booklet contains tips, reminders, and resources along with forms and examples for use in your testing site.

To Test or Not to Test? Booklet
This booklet describes considerations and preparations needed prior to performing waived testing and may assist those who want to implement and oversee waived testing or offer a new test under a CLIA Certificate of Waiver. The booklet contains tips, reminders, and resources along with forms and examples for use in your testing site.

Developing an IQCP - A Step-By-Step Guide
This workbook is designed to assist in developing an IQCP for one or more test systems. Using an example scenario, the workbook guides you through a step-by-step process to develop an IQCP that can be sustained and modified, as needed, over time. You will evaluate your current quality activities and develop an IQCP worksheet which, when completed, can serve as your IQCP document. The approach outlined in this workbook is not mandatory or the only format for documentation but is one example that can be used.

 

Test Categorization

The Food and Drug Administration (FDA) has the authority to implement CLIA test complexity categorization. The FDA also has the authority to grant Emergency Use Authorization (EUA) for tests that have not yet been categorized.

FDA CLIA database Online database of FDA approved laboratory testing and their respective categorization.

FDA EUA databaseFDA online database of all testing granted EUA.

 

Websites

CMS.gov/CLIA
The official website of the Clinical Laboratory Improvement Amendments (CLIA).

CLIA Code of Federal Regulations 42 CFR 493 View the federal regulations applicable to all US clinical laboratories.

CLIA Laboratory Lookup Searchable CMS maintained database of CLIA laboratories.

CDC.gov/CLIA The Centers for Disease Control and Prevention’s CLIA website

CMS Laboratory Registry Once a year CMS makes available specific information that is useful in evaluating the performance of laboratories. This list includes laboratories that have been convicted of fraud, had their certificates revoked, persons convicted of violating CLIA requirements, etc.

Contact Information

Department of Licensing and Regulatory Affairs
Bureau of Survey and Certification - CLIA
PO Box 30838
611 W. Ottawa Street, 1st floor
Lansing, MI  48909

CLIA direct line: (517) 241-2648
Bureau main line: (517) 284-0193
Fax: (517) 763-0214
E-Mail: LARA-BSC-CLIA@michigan.gov