CLIA Certification Number: Types, Fees, and Lookup

A CLIA certification number is the 10-character alphanumeric identifier the Centers for Medicare & Medicaid Services assigns to each clinical laboratory location in the United States. Any facility that tests human specimens for diagnosis, prevention, or treatment of disease needs one before it can legally operate or bill for those services. You obtain the number by submitting Form CMS-116 to your state survey agency, and you can look up any existing lab’s number through the CMS Quality, Certification and Oversight Reports (QCOR) system.1Centers for Medicare & Medicaid Services (CMS). CLIA Certification

What the Number Does

CMS uses your CLIA number to track your facility’s compliance history, certificate type, and inspection results throughout the life of the lab.1Centers for Medicare & Medicaid Services (CMS). CLIA Certification The number follows the location permanently and ties every proficiency test, survey outcome, and enforcement action back to one record.

It also has a direct billing function. Medicare requires the CLIA number in Item 23 of the CMS-1500 claim form when you submit paper claims for laboratory testing. If a reference lab actually ran the test, you enter that lab’s CLIA number rather than your own. Claims submitted without the correct number come back as unprocessable.2Centers for Medicare & Medicaid Services. CMS Manual System Pub 100-04 Medicare Claims Processing

Who Has to Have One

Any facility that examines materials derived from the human body to produce information used for diagnosing, preventing, or treating disease. That covers hospitals, independent reference labs, physician offices, pharmacies, public health departments, mobile testing units, and clinics doing point-of-care tests like rapid strep or blood glucose. The obligation applies whether or not you accept Medicare or Medicaid.3eCFR. 42 CFR Part 493 – Laboratory Requirements

Three narrow exceptions exist. Facilities testing exclusively for forensic purposes are not covered. Research labs that test human specimens but never report patient-specific results for clinical use are exempt. And SAMHSA-certified drug testing laboratories are exempt for that drug testing alone; any other testing they perform still needs CLIA certification.3eCFR. 42 CFR Part 493 – Laboratory Requirements

Washington and New York have CLIA-exempt status because their state laboratory programs meet or exceed federal requirements.4Centers for Medicare & Medicaid Services. List of Exempt States Under the Clinical Laboratory Improvement Amendments Labs in those two states apply through the state health department rather than the standard federal process, and applicants should contact the state agency before completing CMS-116.5Centers for Medicare & Medicaid Services. How to Apply for a CLIA Certificate, Including International Laboratories

At-home test kits don’t escape the rule. If a laboratory analyzes the specimen and returns results, that laboratory is the regulated entity and needs a CLIA number. Many home-use tests are classified as “waived,” which qualifies the lab for the lightest certificate, but the certificate is still required.3eCFR. 42 CFR Part 493 – Laboratory Requirements

The Five Certificate Types

Your certificate type must match the most complex test your lab performs. FDA classifies every cleared test as waived, moderate complexity, or high complexity.

  • Certificate of Waiver. Covers tests FDA has classified as simple with a low risk of wrong results, such as urine pregnancy tests and blood glucose monitoring. The main obligation is following the manufacturer’s instructions.6Centers for Disease Control and Prevention. Waived Tests – Laboratory Quality
  • Certificate for Provider-Performed Microscopy (PPM). Allows physicians and certain midlevel practitioners to perform a limited set of moderately complex microscopy procedures during patient visits, such as urine sediment exams or wet mounts.
  • Certificate of Compliance. Required for moderate or high complexity testing when a state survey agency or CMS will inspect your lab.
  • Certificate of Accreditation. The alternative to a Certificate of Compliance for non-waived testing. A CMS-approved private accrediting organization reviews your lab instead of a government inspector.7Centers for Medicare & Medicaid Services. List of Approved Accreditation Organizations Under CLIA
  • Certificate of Registration. Temporary. Lets you begin non-waived testing while awaiting your initial inspection or accreditation verification.8Centers for Medicare & Medicaid Services. Form CMS-116 – CLIA Application for Certification Instructions

If your lab holds a Certificate of Waiver and you want to start performing non-waived tests, you have to upgrade. That means a new application and the more rigorous personnel, quality control, and proficiency testing requirements that come with higher-complexity testing.3eCFR. 42 CFR Part 493 – Laboratory Requirements Choosing accreditation over government inspection does not reduce your compliance obligations. CMS can still conduct unannounced validation or complaint inspections of accredited labs at any time.9eCFR. 42 CFR Part 493 Subpart Q – Inspection

How to Apply

The application goes through your state survey agency, not CMS headquarters.

  • Complete Form CMS-116. This federal Application for Certification asks for your lab’s location, the testing you plan to perform, your estimated annual test volume, and your laboratory director’s qualifications. Leave the CLIA identification number field blank on an initial application; the number is assigned during processing.8Centers for Medicare & Medicaid Services. Form CMS-116 – CLIA Application for Certification Instructions
  • Submit to your state agency. Mail or deliver the form to the state agency CMS has designated for your state. Do not send payment with the application.5Centers for Medicare & Medicaid Services. How to Apply for a CLIA Certificate, Including International Laboratories
  • Receive your CLIA number and fee coupon. Once the state agency processes the application, you receive a fee remittance coupon showing your newly assigned CLIA identification number.1Centers for Medicare & Medicaid Services (CMS). CLIA Certification
  • Pay the biennial certificate fee using the coupon.

If you applied for a Certificate of Compliance or Certificate of Accreditation, you initially receive a temporary Certificate of Registration so you can begin non-waived testing while waiting for the on-site inspection or accreditation verification.8Centers for Medicare & Medicaid Services. Form CMS-116 – CLIA Application for Certification Instructions

Current Fees

CMS sets CLIA fees, and they’re payable every two years. The mid-2024 schedule:10Centers for Medicare & Medicaid Services. CLIA Certificate Fee Schedule

  • Certificate of Waiver: $248
  • Certificate of Registration: $123
  • Certificate of Compliance or Accreditation: $223 to $11,801, depending on annual test volume and number of specialties

The $223 floor applies to labs performing 10,000 or fewer tests annually. High-volume labs running more than one million tests per year pay the top rate. Some states charge a separate state laboratory license fee, so check with your state health department for anything additional.

Multiple Sites and Mobile Testing

The general rule is one CLIA number per physical location. Each site where testing occurs needs its own application and certificate. Three configurations get exceptions:3eCFR. 42 CFR Part 493 – Laboratory Requirements

  • Mobile and temporary sites. Testing at health fairs, mobile units, or other temporary locations can operate under the certificate of a designated primary site or home base.
  • Hospital campuses. Hospital laboratories in contiguous buildings on the same campus under common direction may share a single application.
  • Limited public health testing. Nonprofit or government labs performing no more than 15 moderately complex or waived tests combined can file one application covering multiple locations. Only labs holding a registration certificate, PPM certificate, certificate of compliance, or certificate of accreditation qualify.

Looking Up an Existing CLIA Number

CMS maintains a public lookup through the Quality, Certification and Oversight Reports (QCOR) system. You can search by laboratory name, address, or CLIA number to verify a lab’s certification status, certificate type, and expiration date.11Centers for Medicare & Medicaid Services. Laboratory Demographics Lookup and Registry The old CDC laboratory search tool was retired in January 2024 and now redirects to the CMS system.12CDC Archive. CDC Has Retired the Laboratory Search Tool

The QCOR lookup is the tool you’ll want when verifying a reference laboratory’s credentials before sending specimens, or when a billing form requires the performing lab’s CLIA number. If a facility doesn’t show up, contact your state survey agency.

Keeping the Number Active

Every type of CLIA certificate expires after no more than two years.3eCFR. 42 CFR Part 493 – Laboratory Requirements CMS sends renewal notices before expiration, but tracking the date yourself is safer. A lapsed certificate means you cannot legally perform testing or receive reimbursement until it’s renewed.

Between renewals, you must notify your state agency within 30 days of any change to ownership, name, location, or director. Labs performing high-complexity testing must report technical supervisor changes within the same 30-day window.3eCFR. 42 CFR Part 493 – Laboratory Requirements Missing this deadline is one of the easier ways to fall out of compliance, and it happens more often than you’d expect when a director leaves and administrative staff don’t realize the clock has started.

Compliance Obligations Tied to the Number

Laboratory Director

Every CLIA-certified lab performing non-waived testing must designate a laboratory director. The director is accountable for the lab’s entire operation: hiring qualified personnel, ensuring test methods produce reliable results, maintaining quality control, and enrolling the lab in proficiency testing.13eCFR. 42 CFR 493.1445 – Standard: Laboratory Director Responsibilities

The director must be on-site at least once every six months, with a minimum of four months between visits, and must document each visit. Between visits, the director has to remain accessible by phone or electronically. No individual may serve as director for more than five laboratories.13eCFR. 42 CFR 493.1445 – Standard: Laboratory Director Responsibilities Qualifications are tiered, with the strictest paths for bachelor’s-degree holders and automatic qualification for board-certified pathologists.14eCFR. 42 CFR 493.1405 – Standard: Laboratory Director Qualifications

Inspections

Labs holding a Certificate of Compliance are inspected biennially, though CMS can schedule inspections more frequently if concerns arise. Labs with a Certificate of Accreditation are inspected by their accrediting organization on the organization’s schedule, and CMS keeps the right to conduct unannounced validation or complaint inspections. Labs holding only a Certificate of Waiver or PPM certificate are not subject to routine biennial inspections, but CMS can inspect them on a complaint or where it identifies an imminent risk to public health.9eCFR. 42 CFR Part 493 Subpart Q – Inspection

Proficiency Testing

Labs performing non-waived testing must enroll in a proficiency testing program approved by the Department of Health and Human Services. The program sends test samples, typically three times per year, and your lab analyzes them as you would patient specimens. Results are scored against expected outcomes.15Centers for Medicare & Medicaid Services. Proficiency Testing and PT Referral Brochure

Failing proficiency testing for the same analyte or subspecialty in two consecutive events, or two out of three events, counts as “unsuccessful participation.” CMS can suspend or limit your certificate and halt Medicare and Medicaid reimbursement for six months. Sending proficiency testing samples to another lab for analysis is treated as intentional fraud and can result in certificate revocation for at least one year.15Centers for Medicare & Medicaid Services. Proficiency Testing and PT Referral Brochure

Penalties

CMS can suspend, limit, or revoke a certificate when a lab’s owner, operator, or employee has misrepresented facts to obtain certification, performed testing outside the scope of the certificate, failed to comply with performance standards, or refused an inspection.16GovInfo. 42 CFR 493.1840 – Suspension, Limitation, or Revocation of Any Type of CLIA Certificate

Civil monetary penalties for deficiencies that pose an immediate threat to patient health range from $8,010 to $26,262 per violation. For deficiencies that don’t rise to immediate jeopardy, penalties run from $132 to $7,877.17Federal Register. Annual Civil Monetary Penalties Inflation Adjustment The amounts adjust annually for inflation and can be imposed per day or per violation.

Intentional violations carry criminal consequences. A first conviction can result in up to one year of imprisonment, a fine, or both. A second or subsequent conviction raises the maximum imprisonment to three years.18Office of the Law Revision Counsel. 42 USC 263a – Certification of Laboratories

Revocation itself requires an administrative law judge hearing where the lab can contest the findings. Where deficiencies pose immediate jeopardy, or where the lab has refused an inspection or refused to provide requested information, CMS can suspend or limit the certificate before that hearing.16GovInfo. 42 CFR 493.1840 – Suspension, Limitation, or Revocation of Any Type of CLIA Certificate If the Office of Inspector General excludes a lab from Medicare, CMS automatically suspends the CLIA certificate for the duration of the exclusion.