What CMS’s New Changes to CLIA Fee Coupons Mean for You

The Centers for Medicare and Medicaid Services (CMS) has made an announcement that it is improving the Clinical Laboratory Improvement Amendments (CLIA) program by switching to electronic fee coupons and CLIA certificates by March 1,2026. This announcement has a direct impact on laboratories and healthcare professionals and how they manage their certification costs. This blog aims to provides an in-depth analysis of these updates, and their implications, and explains how Shoreline Medical Billing Company can assist you in adapting these changes effectively.

Understanding CLIA Certificates and Their Role in Healthcare

The Clinical Laboratory Improvement Amendments of 1988 (CLIA) are federal laws and regulations that are applicable to all US and CLIA-certified international laboratories that performs test on human specimens (e.g., blood, tissue, and body fluid) to diagnose the underlying health conditions.

What is a CLIA Certificate?

These are the certificates issued by CMS to all the laboratories that perform even a single test on human samples for diagnosis purposes. It authorizes them to operate legally within the federal regulations. The main aim of this certification is to ensure that these laboratories have the standards to conduct accurate, safe and reliable tests within the given time. Because these results have a direct impact on the patients’ health and treatment plans.

There are some exceptions to CLIA certification even if the testing is done on human specimen such as

Forensic Testing laboratories for criminal Investigations.
Research Labs whose results are not used for clinical purposes.
Employment related Drug Testing performed by Substance Abuse and Mental Health Services Administration (SAMHSA).
Also, the laboratories located in New York or Washington states may not require a CLIA certificate because these states have their own HHS approved regulatory for laboratories.

Types of CLIA certificates:

They are categorized based on the type and complexity of the tests performed.

Waived Tests	Waived Tests Simple tests with low risk of an incorrect result. Tests for determining the Glucose, Uric Acid, FSH, LH, HDL Cholesterol etc are few examples for waived tests.	Tests for determining the Glucose, Uric Acid, FSH, LH, HDL Cholesterol etc are few examples for waived tests.
Non-Waived Tests	Tests that are moderate to highly complex	Tests performed to detect the presence of bacteria, fungi, virus etc, comes under non-waived tests.

Certificate of Waiver (CoW): This is issued to a laboratory that performs only waived tests.
Certificate for Provider-performed Microscopy (PPM) procedures: This is issued to a laboratory where a qualified physician performs the specific microscopy procedures of moderate complexity during a patient’s visit.
Certificate of Registration (CoR): It is issued to the laboratory to conduct nonwaived moderate to high complexity testing.
Certificate of Compliance (CoC): It is issued to a laboratory that performs nonwaived moderate and high complexity testing after the State Agency (SA) or CMS surveyors conduct a survey and determine that the laboratory is following the applicable CLIA requirements.
Certificate of Accreditation (CoA): It is issued to a laboratory that performs nonwaived moderate and high complexity testing and is based on the laboratory’s accreditation by a CMS-approved accreditation organization (AO).

Steps involved for obtaining a CLIA Certificate:

Step 1: The laboratories must first fill their details and complete the CLIA application (Form CMS-116) available online. Give the laboratory’s latest email address to get email notifications from CMS as well as electronic CLIA certificates and fee coupons.
Step 2: Sending the completed CLIA application to the corresponding State Agency.
Step 3: You will receive the fee coupon mentioning the total amount payable along with a CLIA Identification number. It is a unique 10-digit alphanumeric number used to identify and track the history of the laboratories. We can use this number to make payments, contact SA or CMS for any queries.
Step 4: The applicable fees can be paid by check or via the government portal for payment a secure online platform.
Step 5: Receiving the certificate.

We can get more information regarding the certification procedure through the CMS CLIA certification guide, updated May 2025.

Fees Structure:

All CLIA certificates must be renewed for every 2 years, and the laboratories must pay for registration and survey depending on the certification they hold. This table will help you understand the fee structure that is payable.

For CoW or PPM Certificate

Just the Waiver fee or PPM fee no registration or compliance fee is required.

For CoC Certificate

One time Registration fee: For enrolment and getting the CoR Certificate.

Compliance survey fee: Charges for conducting the survey by SA, to check that the laboratory is following the CLIA Requirements.

Compliance certificate fee: Once the laboratory qualifies this fee is paid to obtain the CoC Certificate.

If the survey finds any discrepancies, it must be addressed and only after that the CoC Certificate will be processed.

For CoA Certificate

One-time registration fee: For enrolment and getting the CoR Certificate. Accreditation certificate fee and a validation survey fee: Charges for accreditation by an AO.

The Recent CMS Updates to CLIA Fee Coupons:

The CMS is planning to go paperless effective from March 1,2026. All laboratories and providers are mandated to apply and get electronic notifications for their CLIA fees coupons and certificates. They will not send the paper coupons or certificates after this date. This initiative by CMS will result in quicker turn around time for payment and receipt of the certificates.

How to make this transition?

The first step to get the electronic notification is to update the laboratory’s business mail address with the State Agency or Accreditation Organization. We can follow any one of these methods to get things done.

By sending a written notification to the corresponding State Agency by email. Including all details such as laboratory name, laboratory director or owner’s name, CLIA number, director or designee’s signature and updated mail address.
If you’re an accredited laboratory, then contact the Accreditation Organization and update your email address.
You can also fill the online form CMS-116 and check the box, “Receive notifications including electronic certificates via email”.

The CMS have also announced the following timeline

May 2025-February 2026

For updating their email address with the SA or AO and switch to electronic mode.

March 1, 2026

Effective from this date CMS will no longer send paper CLIA fee coupons or Paper certificates.

March 2026-May 2026

CMA, State Agencies, Accreditation Organizations will work with the laboratories who have not followed this and missed their deadline.

These recent updates mark a significant shift in laboratory certification management towards advanced technology. By adopting new procedures and leveraging the expert support, providers can ensure seamless adherence to federal requirements. Shoreline Medical Billing Company is committed to support healthcare providers through these transitions. Our team offers comprehensive assistance in understanding CMS updates, managing fee payments, and maintaining compliance.

We at Shoreline Medical Billing Company manage all your certification timeline and handle CLIA-related correspondence with ease. We are dedicated in helping healthcare professionals navigate these regulatory complexities with confidence.

FAQs

Q1. Are my existing paper certificates valid?

Yes, the existing paper certificates are valid until March 1, 2026. So laboratories must update their mail address and switch to electronic notification to get the E-certificate.

Q2. Is there any option for making the payment online?

Yes. You can make online payment through Pay.gov by providing the 10-digit CLIA identification number.

Q3. How long will it take to receive my certificate after the payment is processed?

With the updated electronic notification, the certificate will be processed immediately to the email address as soon as the payment gets processed.

Q4. What is the validity of the certificates issued?

CLIA certificates are to be renewed for every 2 years.

Q5. Do we get notifications or reminders regarding the renewal?

Yes. You will receive a renewal invoice 6 months prior to the expiration of the certificate.

Q6. Is ShorelineMB the same as Shoreline Healthcare Technologies?

Yes, ShorelineMB.com is the official website of Shoreline Healthcare Technologies, a leading provider of medical billing and RCM services.

Sharanya Rajmohan

Content Writer

Sharanya brings clarity to the complexities of medical billing and healthcare regulations. With a knack for turning industry shifts into straightforward, actionable insights, her blogs help readers stay informed without the jargon.

Reach out today for any tailored guidance or assistance in managing your CLIA certificates and fee payments.

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