Did you know that, as of 2024, 317,545 laboratories are currently registered with CLIA, including both exempt and non-exempt facilities?
The Clinical Laboratory Improvement Amendments (CLIA) of 1988 comprise a set of regulations that apply to all U.S. facilities that test human specimens for health or disease assessment. The Centers for Medicare and Medicaid (CMS), Food and Drug Administration (FDA), and Disease Control (CDC) support these federal standards to ensure quality laboratory testing.
This guide will discuss everything you need to know about this amendment and related certifications, from key requirements to enrollment challenges. So, continue reading!
What is a CLIA Number in Medical Billing?
A CLIA number is a unique 10-digit identifier assigned by CMS to laboratories performing human specimen testing. It is a mandatory requirement for laboratories billing for testing services to Medicare, Medicaid, and other commercial payers, and ensures compliance with federal quality standards.
CLIA Certificate Types
Let’s review different types of Clinical Laboratory Improvement Amendments certificates:
1. Certificate of Waiver (CoW)
It is a common certificate required by small clinical laboratories. With this under your belt, you can perform all waived tests.
For context, waived tests are so simple that they have an insignificant risk of erroneous results. These include fecal occult blood, dipstick urinalysis, etc.
2. Certificate for Provider-Performed Microscopy (PPM)
If you are a laboratory that houses physicians, mid-level practitioners, or dentists to perform moderate-complexity microscopic exams, you need this CLIA certification.
With a certificate of PPM, you become eligible to perform all waived tests plus specific microscopic exams, such as potassium hydroxide (KOH) preparations, wet mouths, etc.
3. Certificate of Registration (CoR)
It is a temporary certificate issued to laboratories until CMS can determine if a specific center is in full compliance with CLIA regulations. Under this certification, laboratories can conduct non-waived moderate and high-complexity tests.
You can only receive this certification if you apply for a certificate of compliance or a certificate of accreditation.
4. Certificate of Compliance (CoC)
CoC is issued to laboratories that conduct moderate to high-complexity testing. It is awarded only after an inspection by a state agency (SA) or a CMS surveyor that determines that the laboratory is in full compliance with CLIA requirements and federal regulatory standards.
5. Certificate of Accreditation (CoA)
Note that the inspection must be carried out by a CMS-approved accreditation organization (AO):
What happens when you are a laboratory that conducts moderate to high-complexity testing, but prefers to be inspected by a private, non-profit accreditation organization? You receive CoA instead of CoC.
Listed below are some of the CMS-approved AOs:
- Association of the Advancement of Blood and Biotherapies (AABB)
- American Association for Laboratory Accreditation (A2LA)
- Accreditation Commission for Health Care Inc. (ACHC)
- American Society for Histocompatibility and Immunogenetics (ASHI)
- Commission on Laboratory Accreditation (COLA)
- College of American Pathologists (CAP)
- The Joint Commission (TJC)
How to Get a CLIA Certificate?
Do you want to become a CLIA-certified laboratory? Discussed below is the process by which you can acquire one:
Step 1: Complete Form CMS-116
Download and fill out the CLIA Application for Certification (Form CMS-116). When completing the form, ensure that you use a business email address that multiple staff members can access for electronic notifications and certificates.
Step 2: Submit to the SA
Once you complete the CMS-116 form, send it to the SA in the state where the laboratory is located. You can do it either by email, mail, or fax. However, note that email is the preferred medium.
Step 3: Receive a Fee Coupon
You will receive a fee coupon that includes a unique 10-character alphanumeric CLIA identification number to pay the applicable certification fee.
Note that you can use this number to track your laboratory’s history and for all future payments.
Step 4: Pay the Certification Fee
You can pay the CLIA certification fee using any of the following methods:
- Online (Preferred): Through the U.S. Treasury platform using a bank account (ACH), debit, or credit card.
- By Mail: Send a check along with the paper fee coupon. However, effective from March 1, 2026, CMS will not issue any CLIA paper fee coupons and physical certificates.
Online payments get processed overnight, while check processing may take up to 10 days. Besides, you must pay the fee every two years to maintain the certificate.
Step 5: Receive the Certificate
As soon as payment is received, the official CLIA certificate is issued. In most cases, you are allowed to start testing once the certificate is in hand. However, it is recommended to check with your local SA since some states may have additional local requirements.
CLIA Requirements
Before we discuss the essential requirement, note that receiving this certification is mandatory for laboratories. That is, any facility that tests human specimens, whether to assess patient health or diagnose, prevent, or treat a disease, must be CLIA-certified.
The following is the key criterion for obtaining and maintaining a CLIA certification:
Laboratory Director
The laboratory director has ultimate responsibility for managing the operations and ensuring compliance. A director can manage up to five non-waived laboratories simultaneously.
Qualification Requirements
For high-complexity testing, the director must hold a doctoral degree in biological, physical, chemical, or clinical laboratory science from an accredited institution.
Technical Supervisor
This role is specifically required for high-complexity CLIA-certified laboratories, while moderate-complexity laboratories use a technical consultant. The technical supervisor is responsible for the technical and scientific supervision of the laboratory.
Qualification Requirements
Qualifications of a technical supervisor for high-complexity testing are defined by these core requirements:
- Pathologist: MD/DO/DPM licensed in the state and certified in anatomic or clinical pathology.
- Doctoral/Master’s Degree: Degree in chemical, biological, or clinical lab science with 1 to 2 years of laboratory experience in high-complexity testing for the specific specialty.
- Bachelor’s Degree: Degree in lab science plus 4 years of laboratory experience in high-complexity testing for the applicable specialty.
Specialty-Specific Mandates
Specialties like cytology, histopathology, and clinical cytogenetics typically require an MD/DO/PhD, often excluding those with only a bachelor’s or master’s degree, regardless of their years of experience.
Laboratory Technical Personnel
Laboratory testing personnel are responsible for performing the tests and reporting the results.
Qualification Requirements
Qualifications for these personnel follow a sliding scale where higher education reduces the required experience in high-complexity testing.
- Pathologists (MD/DO): Qualified via board certification.
- Other Doctors (MD/DO/DPM/PhD): Require 1 year of specialty experience.
- Master’s Degree: Requires 2 years of specialty experience.
- Bachelor’s Degree: Requires 4 years of specialty experience.
Specialty-Specific Restrictions
Certain specialties, such as cytology, histopathology, and histocompatibility, have strict requirements to ensure CLIA compliance, typically mandating a pathologist or a doctor (MD/DO/PhD) with several years of highly specialized training.
Licensing and Availability
The laboratory technical personnel must hold a current state license.
Application Requirements
You must complete and submit the CMS-116 form with up-to-date contact information and a business email address.
State-Specific Compliance
Since the requirements for this certification can vary across states, you must check with your local SA before applying.
Adherence to Test Complexity
You must always strive to obtain the certificate type that corresponds to the most complex category of testing you conduct at your laboratory.
Instruction Compliance
If your facility performs waived tests, then you must follow the manufacturer’s instructions for each test system.
Validity Requirements
You must pay a biennial fee to maintain a valid CoC and CoA certification. However, CoW and PPM certificates do not require any registration or compliance fees.
Biennial Inspections
Laboratories with a CoC or CoA must undergo an inspection every two years to ensure they meet quality standards.
30-Day Change Notification
In case of any changes to ownership, name, location, or the laboratory director, you must notify the specific SA within 30 days.
Location Requirements
Each physical location requires a separate certificate where testing is performed, unless a specific multiple-site exception applies. These include:
- Laboratories with no fixed location, such as mobile units, health screening fairs, and other temporary testing locations.
- Facilities that perform limited public health testing. That is, the facility conducts at max a combination of fifteen moderately complex or waived tests per certificate.
- Laboratories that are located within a single hospital with the same laboratory director.
CLIA-Related Challenges Impacting Medical Billing
The following are some of the major challenges associated with CLIA in medical billing:
The 2026 Paperless Shift
Note that, effective from March 1, 2026, CMS will eliminate all CLIA paper fee coupons and physical certificates.
This brings a new challenge for laboratories that have not updated their contact email with their SA. How? Because CMS will send notifications, fee coupons, and certification electronically via email.
Thus, failing to update your email address with the SA will result in missing renewal notices, leading to denials stemming from expired certificates. These denials strain your revenue cycle because you cannot appeal them.
Moreover, failure to use the digital portal of the U.S. Treasury (pay.gov) to pay all fees will result in an unpaid status. This will trigger an automatic billing freeze for all Medicare/Medicaid lab claims.
Complexity Mismatch Denials
Insurance payers use automated edits to cross-reference procedural codes with the certificate level.
Thus, if a facility with a CoW bills for a moderate or high-complexity test even by mistake, it will result in a denial under CARC code B23. This denial code indicates that the billed service is not authorized for the awarded CLIA level.
Missing QW Modifiers
Many waived tests require the QW modifier to signify they are CLIA-waived. However, medical billing software often fails to auto-populate it. As a result, you may receive denials for simple tests, such as rapid flu tests or certain lipid panels.
Location-Specific Issues
What happens when a facility moves or adds a satellite location and fails to notify its local SA within 30 days? Remember that CLIA certificates are linked to a specific physical address. Thus, any claims submitted from the new location will result in a denial.
Referral Lab Confusion
Sometimes a clinic collects a sample but sends it to a reference lab. However, the billing rules for using modifier 90 and reporting the other laboratory’s CLIA number are intricate. This leads to invalid provider or duplicate billing denials.
Box 23 Placement Errors
You must enter the 10-digit CLIA number in box 23 of the CMS-1500 claim form. If the billing system places it in the wrong field or omits the X4 qualifier on electronic claims, the payer’s system will reject the claim even before it reaches a human reviewer.
Partner with MediBillMD to Streamline Laboratory Billing
Even after successfully acquiring a CLIA certification, you can still face claim denials for several reasons. When this happens, and aging accounts receivable start to turn into unnecessary write-offs, it means something is seriously wrong with your billing workflow.
Take a deep breath and initiate an internal audit to determine the root cause of revenue leakage. Do not have time and want a better option? Outsource laboratory billing services to professionals, like MediBillMD. The best part? We also offer a free billing audit, so it will be a win-win situation for you!
