How to Apply for a CLIA Certificate of Waiver: A Step-by-Step Guide for Medical Practices
A CLIA Certificate of Waiver allows medical practices to perform laboratory tests classified as waived under the Clinical Laboratory Improvement Amendments (CLIA). Offering these tests in-house can improve patient convenience, provide results during the visit, and support timely clinical decisions.
Before beginning testing, practices must verify that their intended test systems qualify as waived, obtain the appropriate CLIA certificate, and meet applicable state requirements. A Certificate of Waiver authorizes only waived testing, although other CLIA certificate types also permit waived tests.
While the application process is relatively straightforward, inadequate preparation can lead to administrative delays or compliance problems. Understanding the applicable federal and state requirements before submitting your application helps reduce avoidable errors and establishes a sound foundation for point-of-care testing.
Key Takeaways
- A CLIA Certificate of Waiver permits only waived testing. Other CLIA certificate types also permit waived tests.
- Form CMS-116 must be completed accurately and submitted through the appropriate state agency.
- State requirements may exceed federal CLIA requirements.
- A CLIA number alone does not authorize testing. Follow CMS’s certification instructions and separately verify payer billing requirements.
- Quality control logs, staff training records, and adherence to manufacturer instructions remain essential after approval.
Table of Contents
When a CLIA Certificate of Waiver Is Appropriate
A CLIA Certificate of Waiver is appropriate for a medical practice that performs only tests classified as waived. These tests generally have a low risk of incorrect results when performed according to the manufacturer’s instructions. Practices must verify the classification of each specific test system rather than assuming all point-of-care tests qualify.
Practices planning to perform provider-performed microscopy procedures or other nonwaived testing may need a different CLIA certificate and must meet additional requirements. The appropriate certificate depends on the testing performed, not simply the type of medical practice. For a detailed comparison of the five certificate types, see CLIA Certification vs. Waiver: Understanding Laboratory Requirements.
For many independent medical organizations, remaining strictly within the scope of a Certificate of Waiver is a strategic operational decision. It allows a practice to provide convenient, real-time diagnostic services. It also minimizes the heavy administrative overhead, higher fee schedules, and mandatory biennial inspections associated with moderate- and high-complexity laboratory programs.
Compliance Alert
A Certificate of Waiver reduces regulatory burden but does not eliminate oversight. State agencies may still conduct audits or complaint-driven inspections, making documentation and manufacturer compliance essential at all times.
Follow the manufacturer’s instructions and meet applicable state requirements. Noncompliance can lead to corrective action or enforcement. Billing consequences depend on the circumstances and payer rules; certificate suspension and repayment are not automatic outcomes of every documentation problem.
Step 1: Identify and Document Your Intended Test Menu
Before downloading the application, practices must identify the exact waived tests they plan to offer. This list cannot be a vague generalization; it must match the specific test kits you intend to purchase, as CMS requires cross-referencing with FDA-waived databases.
This upfront planning prevents misalignments among your clinical workflow, inventory management, and revenue cycle. For each test you intend to perform, compile the following operational data:
| Information Needed | Application and Operational Purpose |
|---|---|
| Analyte, test name, and manufacturer | Identify the exact waived test systems in Section VI of Form CMS-116. Verify their classification in FDA’s database. |
| Billing code and modifier requirements | Confirm the appropriate code and applicable payer instructions. Medicare requires QW for many waived test codes, but exceptions exist. These billing checks are separate from the CMS-116 test listing. |
| Manufacturer instructions and kit details | Plan specimen collection, storage, test performance, quality checks, and result reporting around the instructions for the actual system. |
| Estimated annual waived-test volume | Report the estimated total annual volume for waived tests in Section VI. Use a reasonable estimate based on the practice’s planned testing activity. |
Commonly performed waived tests include rapid Group A Strep, visual or digital urine pregnancy testing, blood glucose monitoring via handheld meters, rapid Influenza A+B, and automated urine dipstick analysis. However, waiver status applies to specific test systems rather than general categories, making it essential to cross-reference the manufacturer kit with the FDA database of currently waived analytes before building your menu.
List the waived testing the laboratory performs or plans to perform, as requested on Form CMS-116. Before adding a test, verify its exact classification and manufacturer instructions. Check with your State Agency about reporting changes and any state requirements. Adding nonwaived testing requires the appropriate certificate and additional requirements.
Step 2: Obtain Form CMS-116 and Verify State-Specific Rules
Download the current Form CMS-116 from CMS. It is a fillable application. Review its instructions before entering the laboratory’s information.
For most U.S. laboratories, submit the completed application and required supporting documents to the State Agency where the laboratory is located. Use the CMS CLIA State Agency contact resources to confirm the submission method and destination.
State requirements may include additional forms, licensing, or fees. New York and Washington follow separate state processes. CMS also provides separate instructions for international laboratories. Review the CMS CLIA application instructions and confirm the requirements that apply to your location.
Step 3: Complete the Application with Regulatory Precision
Use the current form and its official instructions. Incomplete or inconsistent information can delay processing or require clarification. Check the certificate selection, testing address, director information, and test menu before submission.
The existing CMS-116 application walkthrough from Lighthouse Lab Services provides broader context. For a Certificate of Waiver, follow the current CMS form instructions and your State Agency’s requirements.
Jennifer walks through Form CMS-116 in this video, recorded in October 2025. The form walkthrough remains useful, but CMS now sends fee notifications and certificates electronically and directs applicants to pay through Pay.gov. Confirm submission instructions with your State Agency and wait until you receive the certificate before beginning testing.
Verify the exact test system’s classification rather than assuming all point-of-care tests are waived. Separately confirm any payer enrollment, certificate submission, and billing requirements that apply to your laboratory.
Section I: General Information
Select “Initial Application” when applying for a new laboratory. Leave the CLIA identification number blank for an initial application. Enter the facility information, testing address, contact details, email address, and laboratory director information requested on the form.
Section II: Certificate Type
Select “Certificate of Waiver” if the laboratory will perform only waived tests. Choose the certificate based on the highest testing complexity the laboratory will perform. Resolve any uncertainty before submitting the application.
Sections III–V: Laboratory Type, Hours, and Multiple Sites
Section III identifies the laboratory type. Section IV records the hours when testing occurs. Section V addresses whether one certificate may cover multiple testing locations under a regulatory exception. Separate locations generally require separate certificates unless an applicable exception allows otherwise. Confirm eligibility with your State Agency.
Section VI: Waived Tests and Estimated Annual Volume
List each analyte, test name, and manufacturer requested in Section VI. Enter the estimated total annual waived-test volume. Attach additional information in the same format when needed. Certificate of Waiver applicants skip Sections VII and VIII.
Sections IX–X and the Application Signature
Complete Section IX for the laboratory’s ownership or control. Section X identifies additional laboratories directed by the same person. Complete the application signature and date as instructed. Confirm any additional state forms or supporting documents before submission.
Laboratory Director Requirements for Waived Testing
A laboratory with a Certificate of Waiver must have a director. Federal CLIA does not require specific education or experience qualifications for that director. State requirements may differ. Confirm applicable state rules rather than applying nonwaived-laboratory director qualifications to every waived testing site.
Step 4: Submit, Pay the Fee, and Receive Your Certificate
Submit the completed and signed application with the supporting documents required by your State Agency. Follow its submission instructions. Pay the federal certification fee after receiving the CMS fee notification. Separate state application or licensing fees may follow different instructions.
Keep a valid email address on file. CMS’s paperless CLIA communications guidance explains that certificates and fee notifications are electronic. The CMS certificate fee schedule lists a $248 biennial Certificate of Waiver fee. Verify the current amount when applying, and check for separate state fees.
Your emailed fee notification includes the laboratory’s unique 10-character alphanumeric CLIA identification number. Pay the fee through Pay.gov using the notification’s instructions. CMS emails the certificate after receiving payment. Its application guidance states that testing may begin once the certificate is received. You can also access and print the certificate through QCOR.
Compliance Alert
Receiving a CLIA number in a fee notification does not mean the laboratory may begin testing. Follow CMS’s certificate issuance instructions and meet applicable state requirements before testing patients. Separately verify payer enrollment, coverage, coding, and claim configuration before billing.
Certification and billing readiness are separate checks. Before submitting claims, verify the laboratory’s certification status, the service date, and the applicable code and modifiers.
Review payer-specific billing policies and reimbursement requirements, including any enrollment or documentation conditions for laboratory services. Configure the CLIA identifier in the required claim field. A Certificate of Waiver does not guarantee coverage or payment.
Building a Post-Approval Compliance Infrastructure
After certification, perform only authorized testing and follow the manufacturer’s instructions for each system. State requirements may add obligations. Use the following operational checks to support reliable results. Specific monitoring and documentation requirements depend on the test instructions and applicable rules.
- Expiration dates: Check test kits, reagents, and controls before use. Remove expired materials from patient-testing supplies.
- Storage conditions: Follow the manufacturer’s temperature and storage instructions. Monitor and document conditions as required for the materials used.
- Quality checks: Run controls at the times and frequencies specified by the manufacturer. Maintain quality control records appropriate to the test instructions and applicable requirements. Investigate unacceptable results before continuing patient testing.
- Staff preparation: Provide staff training before independent testing. Documenting training and periodically checking performance are recommended practices. Do not present federal nonwaived competency requirements as universal requirements for waived testing.
- Test procedures: Follow the instructions for specimen collection, timing, test performance, and result interpretation. Do not assume a modified procedure retains the original system’s waived classification.
The CDC’s waived-testing resources provide recommended practices and a voluntary self-assessment checklist. Confirm additional requirements with your State Agency.
For a broader review of CLIA compliance, quality control, staff competency, and revenue cycle considerations, see our full guide to CLIA waivers and certifications.
Successfully Applying for a CLIA Certificate of Waiver
Navigating the CLIA Certificate of Waiver application is a highly manageable regulatory process when approached with precise, structured documentation. By aligning your clinical test menu with your state-specific rules and completing Form CMS-116 with total accuracy, your practice can avoid unnecessary operational friction.
Operational Snapshot
A CLIA Certificate of Waiver allows practices to bring common diagnostic testing in-house without the extensive oversight required for moderate- or high-complexity laboratories. The greatest operational benefits come from combining accurate enrollment with disciplined documentation, staff training, and adherence to manufacturer protocols.
Build practical procedures around the tests your practice actually performs. Keep manufacturer instructions accessible, maintain appropriate quality control records, and provide staff training before independent testing. Review supplies, certificate expiration, and billing configuration regularly. These steps support reliable testing without confusing waived and nonwaived requirements.
Questions Medical Practices Ask About CLIA Waivers
How long does it take to receive a CLIA Certificate of Waiver?
Processing time varies by State Agency and application completeness. Ask your agency for its current estimate. CMS’s sequence includes application processing, an emailed fee notification containing the CLIA number, payment, and electronic certificate delivery. Receiving the number alone does not mean the certificate has been issued or testing may begin.
Can I perform waived testing before my CLIA number is issued?
No. A CLIA number alone also does not authorize testing. CMS instructs applicants to begin testing after receiving the certificate following payment. Meet applicable state requirements before testing patients. Before billing, separately verify payer enrollment, coverage, coding, modifiers, and required CLIA-number reporting. Certification does not guarantee reimbursement.
Does each practice location need its own CLIA Certificate of Waiver?
What information is required on Form CMS-116?
The application typically requires facility information, ownership details, laboratory director information, certificate type selection, and estimated testing volume. Practices should also identify the waived tests they intend to perform.
How often does a CLIA Certificate of Waiver need to be renewed?
A CLIA Certificate of Waiver is generally valid for two years and must be renewed before expiration to avoid interruptions in testing operations and billing activities.
Can I add additional waived tests after approval?
Yes. Many practices expand their testing menu after receiving approval. Requirements vary by state, so practices should notify the appropriate agency when required and ensure all new tests are FDA-waived.
About the Author
Jennifer Blevens-Smith is the founder and sole consultant driving Integral Clinic Solutions. Armed with deep domain expertise and a commitment to protecting independent medicine, she delivers the personalized, executive-level guidance that healthcare leaders need to build sustainable, high-performing organizations.
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