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​​​​​​​​​​​​​​​​Medi-Cal Enrollment Requirements and Procedures for Pharmacy Providers That Hold A Clinical Laboratory Improvement Amendments (CLIA) Certificate of Waiver​

Frequently Asked Questions from Stakeholder Hearing on June 10, 2025

Below are the answers to most of the questions that the Department of Health Care Services (DHCS) received during the stakeholder hearing on June 10th. If you do not see an answer to your question, please send an email to the appropriate email address(es) listed below: 

Provider Enrollment 

1. What is the time frame for the processing of a new pharmacy application?

​​State law generally requires DHCS to take an action on an application for provider enrollment within 180 days. If an application is returned to a provider to make corrections, the provider has 60 days to resubmit the application. DHCS will have an additional 60 days to review the application once it has been resubmitted. If the application is referred for a comprehensive review, the review timeframe will be extended. Submitting a complete and correct application will reduce DHCS’ overall application processing time.

2. Does a currently enrolled pharmacy provider have to submit a supplemental application to bill for the CLIA waived tests?

Yes, currently enrolled pharmacy providers can submit a supplemental application with a valid copy of their CLIA Certificate of Waiver and a current Certificate of California Clinical Laboratory Registration. The CLIA Certificate of Waiver and the Certificate of California Clinical Laboratory Registration service address must match the service address on the new or enrolled location.

3. Does this provider bulletin only apply to pharmacy providers or does it also include hospitals that have onsite pharmacies with a CLIA license?

This provider bulletin applies to any pharmacy that holds a CLIA Certificate of Waiver and intends to bill Medi-Cal for laboratory services under its pharmacy provider number must comply with the requirements outlined in the bulletin. This includes pharmacies operating as distinct units within a licensed health facility.

4. We are not certified as CLIA waived yet; how long does it take to be certified as CLIA waived Pharmacy?

DHCS does not process the enrollment or issuance of the CLIA Certificates of Waiver. For guidance on how to obtain a CLIA Certificate of Waiver, please visit the Centers for Medicare & Medicaid Services How to Apply for a CLIA Certificate, Including International Laboratories web page.

Additionally, for information on how to obtain a Certificate of California Clinical Laboratory Registration, please visit the California Department of Public Health CLIA Certificate Information web page. 

5. Regarding the CLIA Certificate of Waiver, we do hold a valid certificate, but we do not practice as a lab any longer since the COVID-19 pandemic subsided. Do we have to enroll in the Medi-Cal program?

No, enrollment is not required if you are not performing CLIA-waived tests. The bulletin specifies that effective August 1, 2025, pharmacy providers holding a valid CLIA Certificate of Waiver and a current Certificate of California Clinical Laboratory Registration may bill for CLIA-waived tests within the pharmacist’s scope of practice. However, if your pharmacy no longer performs such tests, enrollment in Medi-Cal for this purpose is not necessary.

6. We do have a CLIA waiver as a lab; is there anything for us to do here?

No, if you are already enrolled as a laboratory, you do not need to submit any additional applications. If you are not a pharmacy provider, these specific enrollment requirements do not apply. The provider bulletin only applies to pharmacy providers with a CLIA Certificate of Waiver. If your lab is not operating as a pharmacy provider, you are not subject to these particular Medi-Cal enrollment procedures included in this provider bulletin.

Federally Qualified Health Centers (FQHC)

1. Would this include clinic sites (FQHC) with a pharmacy permit for a dispensary and with CLIA certification, or does the site need to be specifically a pharmacy?

The enrollment requirements outlined in this bulletin apply specifically to pharmacy providers. The bulletin outlines procedures for pharmacy providers that hold a CLIA Certificate of Waiver, not FQHC’s. If an FQHC clinic site intends to bill for CLIA-waived tests, they are already able to enroll and bill for these services and would not need to take any further action based on this regulatory provider bulletin.

2. What are the enrollment and billing requirements for FQHCs whose pharmacists may want to bill for CLIA waived labs for health centers that (a) have pharmacy carved into their Prospective Payment System (PPS) rate and (b) have pharmacy carved out of their PPS rate?

The requirements depend on whether pharmacy services are included in the FQHC’s PPS rate:

Pharmacy Carved Into PPS Rate: ​If pharmacy services are included in the PPS rate, CLIA-waived lab tests performed by pharmacists must be billed as part of the FQHC encounter. Separate billing for these tests under a pharmacy provider number is not permitted. The FQHC must maintain an active CLIA Certificate of Waiver for the service location where testing is performed.
Pharmacy Carved Out of PPS Rate: If pharmacy services are carved out, the pharmacy must be separately enrolled as a Medi-Cal pharmacy provider and possess an active CLIA Certificate of Waiver for the service location. In this case, the pharmacy may bill Medi-Cal directly for CLIA-waived lab tests in accordance with the scope of practice and all applicable billing requirements.

In both scenarios, CLIA-waived testing must comply with state and federal requirements, including appropriate licensure and scope of practice for pharmacists.​

Benefits

1. What are the CLIA Waiver tests that Pharmacies are now able to perform?

Per Business and Professions (B&P) Code Section 4052.4 (b)(1)(A), these CLIA-waived tests must detect or screen for SARS-CoV-2 (COVID-19) or other respiratory illness, mononucleosis, sexually transmitted infection, strep throat, anemia, cardiovascular health, conjunctivitis, urinary tract infection, liver and kidney function or infection, thyroid function, substance use disorder, or diabetes. 

In addition, pharmacists are allowed to perform other CLIA-waived tests that are waived under the regulations adopted by the federal Health Care Financing Administration and approved by the California State Board of Pharmacy, in conjunction with the Medical Board of California and CDPH, as stated in B&P Code Section 4052.4 (b)(1)(B). The tests that pharmacists may perform must not require the use of specimens collected by vaginal swab, venipuncture, or the collection of seminal fluid.

2. Will this service include the Medi-Cal Medi-Cal Managed Care Organizations (MCOs) and/or Independent Physician Associations (IPAs)?

This provider bulletin applies specifically to providers enrolling in and billing fee-for-service (FFS) Medi-Cal for CLIA-waived tests. Pharmacies seeking to enroll and bill under FFS Medi-Cal must follow the requirements outlined in the bulletin. The bulletin does not apply to providers billing through MCOs or IPAs, which may have separate enrollment and billing processes.

Billing & Reimbursements

1. What are the Medi-Cal reimbursements (fee schedule) for those tests?

For the most current Medi-Cal reimbursement rates for CLIA-waived tests, providers should refer to the M​edi-Cal Rates​ webpage or contact the Medi-Cal Benefits Division at Medi-Cal.Benefits@dhcs.ca.gov​. 

2. Is this carved out FFS similar to Medication Therapy Management (MTM) billing?

Pursuant to Executive Order N-01-19 pharmacy services are carved out, so all pharmacy providers that are billing Medi-Cal for pharmacy services are enrolling in FFS Medi-Cal. Therefore, this bulletin would apply to any pharmacy provider that is enrolled in FFS Medi-Cal, either by submitting a full application for new enrollment or by submitting a supplemental form if the provider is already enrolled. Pharmacy providers will be able to bill FFS Medi-Cal for these services.

This is not similar to MTM. MTM Pharmacy Services must be billed by a Medi-Cal enrolled outpatient pharmacy and the pharmacy must have a signed supplemental contract with the DHCS to provide MTM services.  

3. Can you clarify how the current Medi-Cal fee schedule was developed for pharmacy providers conducting CLIA-waived tests, and whether the rates reflect the actual operational costs and clinical time associated with these services?

In accordance with Attachment 4.19-B, Page 3d, DHCS is authorized to establish or adjust rates for Clinical Laboratory services to not exceed 100 percent of the federal Medicare Clinical Laboratory fee schedule and Medicare Physician fee schedule. For current rates, please refer to the DHCS Clinical Laboratory and Laboratory Services (CLLS) Fee Schedule.

4. Can you clarify if the reimbursed services are for the cost of conducting the CLIA waived test or does it also include the time for clinical assessments and/or provision of treatment or referral based on the results?

Please review the Medi-Cal Pathology: Billing and Modifiers (path bil)​ Billing Manual for more information about billing for CLIA waived tests. 

5. To clarify, we will be able to bill tests for all patients but not a service when a patient has a MCO as their medical plan?

Pharmacies may bill Medi-Cal for CLIA-waived tests only for patients enrolled in fee-for-service Medi-Cal. If a patient is enrolled in a Medi-Cal MCO​, reimbursement for CLIA-waived tests must follow the policies and procedures of that specific health plan. MCOs establish their own provider networks and billing requirements, and coverage of CLIA-waived testing may vary.

Pharmacies should verify the patient’s plan enrollment and contact the applicable MCO to determine if billing for CLIA-waived testing is allowed and under what conditions. ​

6. Who should we contact for questions related to payment and access disparities caused under Assembly Bill (AB) 1114 transfer of responsibilities?

For questions related to payment and access disparities caused under AB 1114, please contact:



Last modified date: 7/30/2025 4:55 PM