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CLIA: Frequently Asked Questions

State of Indiana/Indiana Department of Health (IDOH) CLIA Program Frequently Asked Questions Updated: 2/28/2024

Who needs a CLIA certificate?

Any person or facility that performs laboratory tests on human specimens for the purpose of diagnosis and/or treatment is required by federal law to have a CLIA certificate. Medicare requires the CLIA certificate number before any claims can be processed. Certificates must be renewed every two years for as long as testing is being performed. Changes in ownership, location, and type of testing performed must be reported to the following agency within 30 days of the change.  Please see FORMS section for required forms. Completed forms can be scanned and e-mailed, faxed or mailed to:

FAX: 317-233-7157

E-mail: or

Postal Mail:
Indiana Department of Health
Attn: CLIA Program
2 North Meridian St, Rm 4A
Indianapolis, IN 46201

*** Do not send payment with your application****
It is the facility's responsibility to make sure that the level of testing performed matches the facility's certificate type. Reimbursements by Medicare may be denied if the test submitted does not match the certificate.

What certificate types are available?

Certificate of Waiver
These tests have been approved by the FDA for home use and require very little training to perform. The only requirements for this type of testing are that the manufacturer's instructions are followed exactly and perform only waived tests.  It is recommended that each laboratory follow Good Laboratory Practice including documenting training performed for each person performing tests. Proficiency testing is not required for this level of testing.

Provider Performed Microscopy (PPM)
These are tests performed by a health care provider such as a doctor, physician's assistant, or nurse practitioner. These tests include: microscopic sediment analysis, wet preps, KOH preps, and other microscope based procedures. All waived tests may be performed with this level of certificate with the same requirements as a certificate of waiver. Proficiency testing is not required for this level of testing.

Certificate of Compliance
Tests performed under this type of certificate have been classified as moderate or high complexity and have regulations that are more stringent. Facilities performing moderate or high complexity testing must be enrolled in an approved Proficiency Testing program for each regulated analyte. Analytes that do not have a Proficiency Testing program available must be evaluated at least twice a year. Each facility must establish a Quality Assurance program that includes quality control, personnel policies, patient test management, and proficiency testing. These facilities are inspected every two years to ensure compliance with federal regulations.

Certificate of Accreditation
Facilities with this type of certificate have opted to have a CMS approved accrediting agency perform the biannual inspections instead of CMS for an additional fee. These facilities must follow the accrediting agency's guidelines in addition to the federal regulations. Occasionally, a validation inspection is conducted to evaluate the accrediting agency inspection process.

What are the requirements for testing personnel?

Subpart M contains the personnel sections of the CLIA regulations [Sections 493.1351 through 493.1495]

For tests classified as moderately complex, testing personnel must have at least a high school diploma or G.E.D. and documentation of training before performing tests.

For tests classified as high complexity, testing personnel must have an associate of science degree or higher and documentation of training before performing tests.

All personnel must be evaluated within six months of hire and annually after that.

There are no personnel requirements for waived testing.

To perform PPM testing under the PPM certificate you must be a licensed midlevel practitioner (i.e.  doctor, physician's assistant, or nurse practitioner)

What kinds of facilities are subject to inspections?

All facilities performing laboratory testing are subject to inspection by CMS. Only Certificate of Compliance and Certificate of Accreditation laboratories have routine inspections every two years. Complaint investigations are performed as needed.

What is the Survey or Inspection Process?

The surveyor will schedule routine surveys within six months of the certificate expiration date. Complaints and revisit surveys are always unannounced. The surveyor will review all documents related to laboratory testing including, but not limited to: procedure manuals, test records, personnel files, and patient records. Failure to voluntarily provide this information may result in sanctions against your CLIA certificate and may effect Medicare reimbursements. Facilities are given the opportunity to correct all deficiencies within a specified period. Standard deficiencies must be corrected within a reasonable period not to exceed 12 months.

Does Indiana have any state regulations for laboratories or laboratory personnel?

Currently, the Indiana Department of Health (IDOH) does not license laboratories or laboratory personnel. IDOH does have Communicable Disease and Universal Precautions rules that must be followed.  These rules can be found under Indiana Administrative Code 410 Article 1. Communicable Disease Control:

Other state agencies such Indiana Department of Environmental Management (IDEM) Board of Animal Health may have state statutes and regulations that apply to your laboratory.

CLIA regulations state that only an authorized person may order tests. What does this mean?

CLIA defines an authorized person as someone that has specific authorization from the state in which the test is performed.

REF: S&C-10-12-CLIA

§493.1241 Standard: Test request

(a) The laboratory must have a written or electronic request for patient testing from an authorized person.
Interpretive Guidelines §493.1241(a)
An “authorized person” means an individual authorized under State law to order tests or receive test results, or both. Some states expressly authorize patients to order tests or receive (or give them access to) test results regardless of who ordered the test. In these states a laboratory may release test results directly to a patient as an “authorized person” in accordance with state law.
Patients may also be considered “individuals responsible for using test results” if state law does not expressly prohibit release of test results directly to patients. If the laboratory is requesting payment under Medicare, the laboratory must follow the requirements in the Social Security Act regarding test ordering for Medicare reimbursement.

Indiana does not currently have any statutes that define an "authorized person".

However, the Medicare regulation specifies that the "authorized person" must be a doctor with a current state medical license.

Other sources of information are the Indiana Professional Licensing Agency (IPLA), Indiana Board of Pharmacy, and the Indiana Board of Nursing.

Can patients order their own tests in Indiana?

Yes, this practice is known as Direct Access Testing (DAT) and currently Indiana law does not prohibit patients from ordering their own tests. However, Medicare and Medicaid will not pay for any laboratory testing not ordered by an authorized person.

Specific licensed entities may have additional requirements under their specific license. Such as for hospitals under 410 IAC 15-1-5.3 Laboratory Services (a)(2) “The laboratory performs tests and examines specimens on the written request of individuals and practitioners allow to order such evaluations and receive the results of the evaluations to the extent permitted by law and authorized by the governing body.”

Also, it is up to the laboratory to decide whether or not to provide Direct Access Testing.

How do I renew my CLIA Certificate?

Billing coupons are mailed from the U.S. Department of Health & Human Services, Baltimore, MD. Coupons for CLIA Certificate of Wavier, Certificate of Microscopy and Certificate of Accreditation renewals will be mailed out six months prior to your current certificate expiration date. After full payment is received, your next two year certificate cycle is considered renewed. Your CLIA Certificate will not be mailed to you until approximately 2 weeks before your current certificate expires.

Compliance fee coupons for CLIA Certificate of Compliance renewals are mailed out twelve months prior to your current certificate expiration date. Full payment must be received before a compliance survey will be scheduled by IDOH. Once IDOH performs the survey and determines that your laboratory is compliant with applicable CLIA regulations, a certificate fee coupon will be mailed to you. After full payment of the certificate fee is received, your next two year certificate cycle is considered renewed.

Where do I send my payment for my CLIA Certificate?

Make check payable to:
CLIA Laboratory Program

Mail check to:
CLIA Laboratory Program,
P.O. Box 3056,
Portland, OR 97208-3056

Write your CLIA identification number on the check, and include the billing coupon with your payment.

You can now pay online with your CLIA number and the amount due.  Please follow the instructions below. 


When will I receive my new CLIA Certificate?

Renewed CLIA certificates will be mailed approximately two weeks prior to your current expiration date if full payment of CLIA fees is received. Initial CLIA certificates will be mailed approximately two weeks after full payment of CLIA fees is received.

How do I request changes for my CLIA Certificate?

A new CMS 116 CLIA Application may be completed for any changes.

Please click on the link below and follow the instructions:

Documentation Required for Change for Indiana CLIA Information for Laboratories

**Do not send change requests with your payment. Requests to change facility name, address, tax id, mailing address or laboratory director must be reported to IDOH within 30 days of the change. Requests to change your CLIA certificate type must be submitted on the CMS-116 CLIA Application for Certification BEFORE you perform any tests not covered under your current certificate.

Change request(s) may be faxed, e-mailed or mailed:

FAX: 317-233-7157

E-mail: or

Postal Mail:
Indiana Department of Health
Attn: CLIA Program
2 North Meridian St, Rm 4A
Indianapolis, IN 46201

When applying for a Provider Performed Microscopy Procedure (PPM) Certificate, Certificate of Compliance or Certificate of Accreditation, what additional information/documentation is required?

Change of Director Documentation Needed

Laboratory directors performing nonwaived testing (including PPM) must meet specific education, training and experience under subpart M of the CLIA requirements.  Proof of these requirements for the laboratory director must be provided and submitted with the application.  Information to be submitted with the application may include:

  • Verification of State Licensure, as applicable
  • Documentation of qualifications:
    • Education (copy of Diploma, transcript from accredited institution, CMEs),
    • Credentials, and
    • Laboratory experience.

Individuals who attended foreign schools must have an evaluation of their credentials determining equivalency of their education to education obtained in the United States.  Failure to submit this information will delay the processing of your application.

Please call 317-233-7502 for further information.

Documentation of Laboratory Accreditation:

When submitting an application for a Certificate of Accreditation, you must also submit documentation showing that you have contacted the laboratory accrediting program to seek laboratory accreditation for your laboratory.

Acceptable documentation includes a copy of a letter from the laboratory to the accrediting program requesting laboratory accreditation, a copy of the laboratory accreditation application submitted to the accrediting program, or a welcome letter from the accrediting program to the laboratory.

What are the requirements to qualify as a laboratory director for a Certificate of Compliance or Certificate of Accreditation laboratory?

The regulatory education and training requirements for a laboratory director depend upon the complexity of laboratory testing performed. A state licensed physician who is board certified or board eligible in anatomic or clinical pathology meets the requirements to direct a laboratory of any complexity. All other individuals who wish to direct a laboratory holding a Certificate of Compliance or a Certificate of Accreditation should call 317-233-7502 for further information.

Laboratory Director Qualifications:

Subpart M contains the personnel sections of the CLIA regulations [Sections 493.1351 through 493.1495]

Certification Boards for High Complexity Laboratory Directors:

CME Credits for Moderately Complex Laboratory Directors:

Can I have more than 1 location under the same CLIA number?

CLIA certificates are location specific.  Therefore, if you perform testing at more than one location then you will have more than one CLIA certificate unless you qualify for a multi-site site exception and complete a CMS 116 application for the multi-site exception.  To qualify for a multi-site exception your laboratory must meet one of the below criteria:

  1. Temporary Testing such as a health fair may file a single application.
  2. A not-for-profit or Federal, State, or local government laboratory engaged in limited public health testing (no more than 15 total tests for all sites, waived or moderately complex) may file a single application.
  3. Laboratories with in a hospital that are located in contiguous buildings on the same campus and that are under common direction may file a single application.  Hospital satellites or auxiliary laboratories located outside a hospital must each make a separate application.

Can I have more than one CLIA number at the same location?

The CLIA regulations [42 CFR 493.35(a), 493.43(a) and 493.55(a)] generally require all laboratories performing waived and non-waived testing to file a separate application for each laboratory locations.  Multiple laboratories may operate at the same physical location (e.g., same building or suite, as applicable) with separate CLIA numbers as long as each laboratory can demonstrate that it is operating as a separate and distinct entity.  Each CLIA certificate represents a laboratory, and each laboratory is responsible for complying with the applicable CLIA requirements.

Multiple laboratories that operate at the same physical location and use the same testing personnel and equipment must meet the following conditions:

  1. All records (e.g., quality control, procedure manuals, and personnel competencies) must be kept separate and distinct for each laboratory and must clearly show that each laboratory is operating independently.
  2. The hours of operation must be specified for each laboratory.
  3. The hours of operation for each laboratory must be separate and distinct.  The times of testing cannot overlap and cannot be simultaneous.

I am no longer performing laboratory testing in my office. How do I terminate my CLIA certificate?

Requests to terminate your CLIA certificate must be submitted in writing to IDOH. Include laboratory name, CLIA number, name of the laboratory director and/or owner, the reason your certificate should be terminated, the effective date of termination, your laboratory contact information and the signature of the laboratory director or his/her designee. Submit requests to:

FAX: 317-233-7157

E-mail: or

Postal Mail:
Indiana Department of Health
Attn: CLIA Program
2 North Meridian St, Rm 4A
Indianapolis, IN 46201

What is the cost for a CLIA certificate?

Certificate of Waiver: $248 for 2 year certificate

Certificate of Provider Performed Microscopy Procedures: $297 for 2 year certificate

Certificate of Compliance or Certificate of Accreditation: Fees depend on the annual test volume and number of laboratory specialties/subspecialties.

For further information, please see


All forms (CMS 116 CLIA Application, Enclosure A Disclosure of Ownership and Enclosure I Methodology Test list) must be completed and signed and appropriate documentation attached for initial certificates and most changes of certificate type.

The CMS 116 CLIA Application and Enclosure A Disclosure of Ownership are completed for change of ownership and Tax ID.

The CMS 116 CLIA Applications may be completed for any changes.

CMS 116 CLIA Application:

Enclosure A Disclosure of Ownership (Also, include documents requested on page 1: IRS letter of Tax ID and Secretary of State Certification)

Enclosure I Methodology Test List


Proficiency Testing: CLIA Approved Proficiency Testing Providers

Additional Information on Proficiency Testing

CLIA Brochure

Calibration and Calibration Verification Procedures

Good Laboratory Practices for Waived Laboratories

How to obtain a CLIA certificate

Laboratory Complaints

Laboratory Director Responsibilities

Laboratory Director Qualifications:

Certification Boards for High Complexity Laboratory Directors

CME Credits for Moderately Complex Laboratory Directors

Verification of Performance Specifications

OSHA Blood Borne Pathogens standards

Individualized Quality Control Plan (IQCP)

Individualized Quality Control Plan (IQCP) Developing an IQCP

Ready Set Test

To Test or Not to Test

What Do I Need to Do to Assess Personnel Competency?