What is CLIA number

Clinical Laboratory Improvement Amendments 

The Clinical Laboratory Improvement Amendments (CLIA), passed by Congress in 1988, established quality standards for all laboratory testing. CLIA ensures the accuracy, reliability, and timeliness of patient test results, wherever a test is performed. A laboratory is defined as any facility that performs laboratory testing on specimens derived from humans for the purpose of providing information for the diagnosis, prevention, treatment of disease, or impairment of, or assessment of health. CLIA is user-fee funded; therefore, all costs of administering the program are covered by the regulated facilities. 

CLIA standards are national and are not Medicare-exclusive. CLIA applies to all providers rendering clinical laboratory and certain other diagnostic services, whether or not claims are filed to Medicare.

CLIA Quality Standards 

CLIA defines quality standards for proficiency testing (PT), patient test management, quality control, personnel qualifications, and quality assurance, as well as specific cytology provisions. The Centers for Medicare & Medicaid Services (CMS) administers CLIA, including laboratory registration, fee collection, surveys, surveyor guidelines and training, enforcement, approvals of PT providers, accrediting organizations, and exempt states. The Centers for Disease Control and Prevention (CDC) are responsible for test categorization and CLIA studies.

CLIA Number 

Upon certification, each laboratory is assigned an individual and unique CLIA number. Each CLIA number consists of ten alphanumeric positions. The CLIA number must be on all claims for laboratory services, or the claim will be returned as un- processable. The CLIA number must be entered in block 23 of Form CMS-1500 or the applicable electronic field.



When is a CLIA Certificate  Required?

NOTE: Congress passed the Clinical Laboratory Improvement Amendments (CLIA) in 1988 establishing quality standards for all laboratory testing to ensure the accuracy, reliability and timeliness of patient test results regardless of where the test was performed. The final CLIA regulations were published in the Federal Register on February 28, 1992. The requirements are based on the complexity of the test and not the type of laboratory where the testing is performed. On January 24, 2003, the Centers for Disease Control and Prevention (CDC) and the Centers for Medicare & Medicaid Services (CMS) published final CLIA Quality Systems laboratory regulations that became effective April, 24, 2003.

DO I NEED TO HAVE A CLIA CERTIFICATE?

CLIA requires all facilities that perform even one test, including waived tests, on “materials derived from the human body for the purpose of providing information for the diagnosis, prevention, or treatment of any disease or impairment of, or the assessment of the health of, human beings” to meet certain Federal requirements. If a facility performs tests for these purposes, it is considered a laboratory under CLIA and must apply and obtain a certificate from the CLIA program that corresponds to the complexity of tests performed.

WHAT IS A WAIVED TEST?

As defined by CLIA, waived tests are categorized as “simple laboratory examinations and procedures that have an insignificant risk of an erroneous result”. The Food and Drug Administration (FDA) determines the criteria for tests being simple with a low risk of error and approves manufacturer’s applications for test system waiver.

HOW CAN I FIND A LIST OF WAIVED TESTS?

For a list of waived tests sorted by analyte name, visit the FDA website at http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfClia/analyteswaived.cfm For a list of waived tests sorted by the test categorization date and by the test system name, visit the FDA website at
http://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfClia/testswaived.cfm.

HOW DO I APPLY FOR A CLIA CERTIFICATE?

The CLIA application (Form CMS-116) is available online at the CMS CLIA website located at the end of this brochure. Forward your completed application to the address of the local State Agency for the State in which your laboratory is located. This information is available online or you may contact the CMS CLIA Central Office. 

ARE THERE ANY STATES THAT EXEMPT ME FROM  HAVING TO APPLY FOR A CLIA CERTIFICATE?

Any laboratory located in a state that has a CMS approved laboratory program is exempt from CLIA certification. Currently, there are two states with approved programs: Washington and New York. New York has a partial exemption; therefore, if your laboratory is located in that state, contact the New York State Agency concerning your need for a CLIA certificate.

IF I HAVE MORE THAN ONE LABORATORY LOCATION, DO I NEED A CLIA CERTIFICATE FOR EACH LOCATION?

You will need a CLIA certificate for each location where you perform testing unless you qualify for one of the exceptions listed below.

● 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.

● Not-for-profit or Federal, State or local government laboratories that engage in limited public health testing, may file a single application.

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

Contact your State Agency if you have questions or you are filing a single application for more than one testing site.


WHEN CAN I BEGIN TESTING?

After you apply for your certificate, you will receive a coupon notifying you of the corresponding fee. Follow the instructions on the fee coupon for payment. After CMS receives your payment, your certificate will be mailed to you. You may begin testing once you have received your certificate containing your CLIA number. However, you need to check with your State Agency since some states have additional requirements.

WHERE CAN I FIND ADDITIONAL INFORMATION AND GUIDANCE?

Refer to the “The State Operations Manual”, Appendix C – Interpretive Guidelines (CMS Publication 7) available on the CMS website at: www.cms.hhs.gov/clia.

Why Is CLIA Important? 

CLIA establishes quality standards for laboratories to ensure the accuracy, reliability, and timeliness of the patient’s test results. CMS data indicates that CLIA helped improve the quality of testing in the United States. The number of quality deficiencies decreased about 40 percent from the first laboratory survey to the second under CLIA. Reviews of PT over time resulted in similar findings.

Does CLIA Apply Only to Laboratories Obtaining Payment Through Medicare?

 CLIA standards apply nationally and not exclusively to Medicare. CLIA applies to all entities providing clinical laboratory services, whether or not they or another provider files Medicare claims for the tests. Laboratories billing Medicare have additional responsibilities and requirements discussed in the Medicare Laboratory Services section.

What Is a Certificate of Waiver (CW)?

 The CW permits a laboratory to perform only waived tests. Waived tests are so simple and accurate that little risk of error exists when done correctly. Examples of waived tests include: ■ Certain testing methods for glucose and cholesterol; ■ Fecal occult blood tests; ■ Pregnancy tests; and ■ Some urine tests. Routine on-site surveys are not required for a CW unless there is a complaint. Along with enrolling in the CLIA program and paying the fee, a laboratory must follow the manufacturer’s instructions for test performance.


CLIA Certification

Clinical Laboratory Improvement Amendments (CLIA) claim edits are applied to all claims for lab services that require CLIA certification. Those claims that do not meet the required criteria will deny.

Claims are edited to ensure payment is not made to:

• providers who do not have a CLIA certificate

• providers submitting claims for services rendered outside the effective dates of the CLIA certificate

• providers submitting claims for services not covered by their CLIA certificate Louisiana Medicaid maintains a current provider CLIA file. Therefore, providers do not have to include their CLIA certification number on claim forms. In fact, the CLIA certificate number should not be entered on the claim form for Medicaid services.

Providers must submit a copy of the CLIA certification to Unisys Provider Enrollment initially to have the certification added to the provider file. Once the CLIA certification has been added to the file, certification updates are done automatically via CMS’s file updating process (OSCAR) and are sent to Medicaid without provider involvement.


Providers with regular accreditation, partial accreditation, or registration certificate types are allowed by CLIA to bill for all lab codes.

Providers with waiver or provider-performed microscopy (PPM) certificate types shall be paid for only those waiver and/or provider-performed microscopy codes approved for billing by CMS. Providers with waiver or provider-performed microscopy (PPM) certificates wishing to bill for codes outside their restricted certificate types should obtain the appropriate certificate through Health Standards. If the certificate type is upgraded, claims can be paid only for dates of service that fall within the upgraded certification dates.

Providers are notified of additions and deletions to the CLIA file through Louisiana Medicaid Provider Update and remittance advice messages. CLIA information can also be obtained on the Louisiana Medicare website at www.lamedicare.com using the CLIA link. 


The Medical Review Department is responsible for several functions, including postprocedural review of claims for manually priced procedures and designated procedures and diagnoses which require medical documentation to ensure compliance with Medicaid policy.


CLIA FAQs from Empire BLUE



What are the Clinical Laboratory Improvement Amendments?

The Clinical Laboratory Improvement Amendments (CLIA) establish quality standards for all non-research laboratory testing performed on specimens derived from humans for the purpose of providing information for the diagnosis, prevention, treatment of disease, or impairment of, or assessment of health. CMS administers the CLIA laboratory certification program.

Why did Empire start requiring CLIA certification in July 2015? Empire wants to help ensure claims are properly coded and align with CMS requirements.

If the CLIA number is not present on the claim form will the claim deny?

Yes. The claim will deny back to the submitter if the CLIA number is missing or invalid. The missing or invalid CLIA number will be denied with denial Code GLI.

What field should a provider use to bill their CLIA certification number?

The CLIA number is located in the following fields according to claim type:

• Electronic Data Interchange (EDI) format -- Loop 2300, REF01 = X4, REF02

• CMS 1500 Paper Form – Field 23

How should a provider bill a claim that requires more than one CLIA certification or a prior authorization number and CLIA certification? 

If billing more than one item in field 23 of the CMS 1500 form, the provider must include a hyphen (-) or semicolon (;) between the items.


Box 23: Your CLIA number * 

Box 23

• Electronic claims – Contact your TearLab Reimbursement Advocate. TearLab will provide oneon-one assistance to ensure the CLIA number is transmitting in the required electronic data format.

• ANSI 5010 E-claim Crosswalk

In loop 2300, Segment REFO2, enter the CLIA Certification number (Do not enter “CLIA” with the certificate number as this will cause claims to deny as an invalid identification number). CLIA Crosswalk – CMS1500 to E-claim Format


Claim!Description Loop Segment Electronic!Description 23. Prior!Authorization!number 2300 REF01 Reference!identification!qualifier!=X4 REF02! CLIA!Certification!number


When is a CLIA Certificate Required?

NOTE: Congress passed the Clinical Laboratory Improvement Amendments (CLIA) in 1988 establishing quality standards for all laboratory testing to ensure the accuracy, reliability and timeliness of patient test results regardless of where the test was performed. The final CLIA regulations were published in the Federal Register on February 28, 1992. The requirements are based on the complexity of the test and not the type of laboratory where the testing is performed. On January 24, 2003, the Centers for Disease Control and Prevention (CDC) and the Centers for Medicare & Medicaid Services (CMS) published final CLIA Quality Systems laboratory regulations that became effective April, 24, 2003.

DO I NEED TO HAVE A CLIA CERTIFICATE?

CLIA requires all facilities that perform even one test, including waived tests, on “materials derived from the human body for the purpose of providing information for the diagnosis, prevention, or treatment of any disease or impairment of, or the assessment of the health of, human beings” to meet certain Federal requirements. If a facility performs tests for these purposes, it is considered a laboratory under CLIA and must apply and obtain a certificate from the CLIA program that corresponds to the complexity of tests performed.

WHAT ARE THE DIFFERENT TYPES OF CLIA CERTIFICATES AND HOW LONG ARE THEY EFFECTIVE?

All types of certificates are effective for two years and the different types of certificates are:

** Certificate of Waiver (COW): Issued to a laboratory that performs only waived tests. 

** Certificate for Provider Performed Microscopy (PPM) procedures: Issued to a laboratory in which a physician, midlevel practitioner or dentist performs specific microscopy procedures during the course of a patient’s visit. A limited list of microscopy procedures is included under this certificate type and these are categorized as moderate complexity.

** Certificate of Registration:

Issued to a laboratory to allow the laboratory to conduct nonwaived (moderate and/or high complexity) testing until the laboratory is surveyed (inspected) to determine its compliance with the CLIA regulations. Only laboratories applying for a certificate of compliance or a certificate of accreditation will receive a certificate of registration.

** Certificate of Compliance (COC):

Issued to a laboratory once the State Department of Health conducts a survey (inspection) and determines that the laboratory is compliant with all applicable CLIA requirements. This type of certificate is issued to a laboratory that performs nonwaived (moderate and/or high complexity) testing

** Certificate of Accreditation (COA):

Issued to a laboratory on the basis of the laboratory’s accreditation by an accreditation organization approved by CMS. This type of certificate is issued to a laboratory that performs nonwaived (moderate and/or high complexity) testing.

There are six CMS-approved accreditation organizations:

** AABB

** American Osteopathic Association (AOA)

** American Society of Histocompatibility and Immunogenetics (ASHI)

** COLA

** College of American Pathologists (CAP)

** Joint Commission on Accreditation of Healthcare Organizations (JCAHO) Contact information for the above CMS-approved accreditation organizations is available on the CMS CLIA web site at www.cms.hhs.gov/clia. If you apply for accreditation by one of the CMS-approved accreditation organizations, you must also apply to CMS for a COA concurrently.

WHAT IS A WAIVED TEST?

As defined by CLIA, waived tests are categorized as “simple laboratory examinations and procedures that have an insignificant risk of an erroneous result”. The Food and Drug Administration (FDA) determines the criteria for tests being simple with a low risk of error and approves manufacturer’s applications for test system waiver.

HOW DO I APPLY FOR A CLIA CERTIFICATE?

The CLIA application (Form CMS-116) is available online at the CMS CLIA website located at the end of this brochure. Forward your completed application to the address of the local State Agency for the State in which your laboratory is located. This information is available online or you may contact the CMS CLIA Central Office.

IS THERE ANY TYPE OF LABORATORY TESTING THAT IS NOT SUBJECT TO A CLIA CERTIFICATE?

Yes, there are some testing exceptions that do not require CLIA certification.

The following exceptions to CLIA certification apply regardless of a laboratory’s location:

** Any laboratory that only performs testing for forensic purposes;

** Research laboratories that test human specimens but do not report patient specific results for the diagnosis, prevention or treatment of any disease or impairment of, or the assessment of the health of, individual patients; or

** Laboratories certified by the Substance Abuse and Mental Health Services Administration (SAMHSA), in which drug testing is performed that meets SAMHSA guidelines and regulations. However, a CLIA certificate is needed for all other testing conducted by a SAMHSA-certified laboratory.

ARE THERE ANY STATES THAT EXEMPT ME FROM HAVING TO APPLY FOR A CLIA CERTIFICATE?

Any laboratory located in a state that has a CMS approved laboratory program is exempt from CLIA certification. Currently, there are two states with approved programs: Washington and New York. New York has a partial exemption; therefore, if your laboratory is located in that state, contact the New York State Agency concerning your need for a CLIA certificate.

IF I HAVE MORE THAN ONE LABORATORY LOCATION, DO I NEED A CLIA CERTIFICATE FOR EACH LOCATION*??

You will need a CLIA certificate for each location where you perform testing unless you qualify for one of the exceptions listed below.

** 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.

** Not-for-profit or Federal, State or local government laboratories that engage in limited public health testing, may file a single application. 

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

Contact your State Agency if you have questions or you are filing a single application for more than one testing site.

You can obtain more information concerning the amount of certificate fees from the CMS CLIA website under “CLIA Certificate Fee Schedule” or from your State Agency. For information concerning compliance (survey) fees, you may contact your State Agency or accreditation organization. These fees are based on the number and types of testing you perform and must cover the cost of the CLIA program because CLIA is entirely user fee funded.

WILL I RECEIVE AN IDENTIFYING CLIA NUMBER?

You will receive a ten-digit number on the CLIA certificate. This number will be utilized to identify and track your laboratory throughout its entire history. You should use this number when making inquiries to the State Agency and CMS about your laboratory.

WHEN CAN I BEGIN TESTING?

After you apply for your certificate, you will receive a coupon notifying you of the corresponding fee. Follow the instructions on the fee coupon for payment. After CMS receives your payment, your certificate will be mailed to you. You may begin testing once you have received your certificate containing your CLIA number. However, you need to check with your State Agency since some states have additional requirements.

DO I NEED TO NOTIFY ANYONE IF I MAKE ANY CHANGES IN MY LABORATORY?

For all types of CLIA certification, you must notify the State Agency or your accreditation organization within 30 days of any changes in:

** Ownership

** Name

** Location

** Director

** Technical supervisor (for high complexity testing only) If you perform only waived tests and wish to add PPM procedures or other nonwaived (moderate or high complexity) testing to your menu, you must reapply for the appropriate certificate using the same form (Form CMS-116) you used for your initial CLIA certification. However, you cannot begin nonwaived testing until you have paid the appropriate fee, and have received the appropriate certificate. 

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