An Analytical Review of the March 2026 Transition, Its Scope, Compliance Obligations, and Operational Implications
By Elena Pak, Credentialing Department, WCH
On March 1, 2026, the Centers for Medicare & Medicaid Services will cease mailing paper CLIA certificates, fee coupons, billing notices, and other program communications to the more than 317,000 certified laboratories operating across the United States. The deadline is firm and the transition is not optional. All CLIA-certified entities — from large academic medical center reference laboratories to small physician office practices running a single point-of-care glucose test — must register to receive electronic communications or risk losing access to their certificates and billing infrastructure.
The stakes are direct: CLIA certification is a legal prerequisite for virtually all clinical laboratory testing performed on human specimens in the United States, and it underpins Medicare and Medicaid payment eligibility. A missed fee coupon or failed renewal notice could translate into compliance violations, suspended testing authority, and lost reimbursement — consequences that ripple outward to the patients who depend on timely diagnostic results.
This article examines the scope and mechanics of the transition, analyzes the populations most at risk of non-compliance, and assesses the broader implications for laboratory operations and federal program oversight.
The Scale of the CLIA Universe
Understanding the significance of this transition requires an accurate picture of the CLIA-certified laboratory landscape. As of March 2024, the CMS CLIA database contained records for more than 317,545 certified laboratory facilities across the country — a number that has grown substantially over the past decade, accelerated in part by the expansion of point-of-care testing during and after the COVID-19 pandemic.
The landscape is dominated by Certificate of Waiver (CoW) holders, which as of March 2024 numbered approximately 244,791 — representing roughly 80% of all non-exempt certified laboratories. These are facilities authorized to perform only the simplest, lowest-risk laboratory tests as categorized by the FDA: dipstick urinalysis, urine pregnancy tests, fecal occult blood tests, blood glucose monitoring, rapid influenza and COVID-19 antigen tests, and similar analyses. Certificate of Waiver holders span an enormous range of care settings. They include independent physician office laboratories, urgent care centers, federally qualified health centers, rural health clinics, school health programs, occupational health offices, dental practices, nursing homes, assisted living facilities, pharmacies, and even some correctional health programs.
An additional 25,682 laboratories hold Certificates for Provider-Performed Microscopy (PPM) procedures, while approximately 16,643 hold full Compliance certificates and roughly 15,894 hold Certificates of Accreditation from CMS-recognized accreditation organizations such as the College of American Pathologists, The Joint Commission, COLA, and others. Together, this ecosystem performs the diagnostic testing that underlies an estimated 70% of all clinical decision-making in American medicine.
The breadth of this regulated universe is crucial context for assessing the paperless transition. While large independent laboratories and hospital systems have robust administrative infrastructure and are well-positioned to manage an operational change of this kind, the majority of CLIA certificate holders are small, resource-constrained organizations — physician practices, nursing homes, rural health clinics — for whom a missed email notification or an outdated contact record could have disproportionate consequences.
What Exactly Is Changing — and What Is Not
The March 1, 2026 transition encompasses two interrelated but distinct shifts: a move to electronic communications and a move to electronic payments.
On the communications side, CMS will no longer mail paper CLIA certificates or paper fee coupons after the deadline. Instead, all of the following will be delivered exclusively by email: CLIA certificates (including initial, renewal, and updated certificates reflecting any changes to the facility), fee coupons notifying laboratories of upcoming certification fees, billing notices and other program communications, and general CLIA program updates. For laboratories that have been on the receiving end of paper communications for decades, this represents a fundamental change in how they monitor and manage their certification lifecycle.
On the payment side, CMS is simultaneously requiring all laboratories to pay their CLIA certification and survey fees online through Pay.gov, a secure platform hosted by the U.S. Treasury Department. Starting March 1, 2026, online payment is mandatory. The agency notes that this transition offers a meaningful operational benefit: payments processed through Pay.gov are handled overnight, meaning certificates can be issued significantly faster than under the paper-based process, which required physical coupon submission and manual processing.
What is not changing — and this is worth emphasizing — is the underlying CLIA regulatory framework itself. Certificate types, renewal cycles, testing complexity categories, proficiency testing requirements, personnel standards, and inspection obligations remain unchanged. The transition is administrative, not substantive. But administrative failures in a regulatory program have regulatory consequences, and that distinction matters less when a laboratory’s certificate lapses.
The Compliance Steps: A Clear but Time-Sensitive Process
CMS has outlined a straightforward process for completing the transition, with multiple pathways available to accommodate different organizational structures.
Laboratories have three primary options for registering to receive electronic communications. The first is to provide written notification directly to their State Agency by email, including the laboratory name, the laboratory director or owner’s name, the CLIA number, and a director or designee’s signature. The second option, relevant for accredited laboratories, is to contact their Accreditation Organization directly — the AO can now add or update email addresses for the laboratories it surveys. The third option is to complete the CMS-116 application form and check the box under the General Information section that reads, “Receive notifications including electronic certificates via email.” This box, easily overlooked in a dense administrative form, is the formal mechanism through which a laboratory opts into electronic communications under the CLIA program.
Beyond registration, laboratories must confirm that the email address on file with their State Agency or Accreditation Organization is current, accurate, and actively monitored. An email address registered to a departed administrator, a defunct departmental inbox, or an individual who has left the organization will effectively replicate the problem that the paperless transition is designed to solve — critical communications going undelivered.
For organizations with multiple laboratory sites operating under separate CLIA numbers, each site must be individually registered. A health system with 20 outpatient laboratory locations, each holding its own Certificate of Waiver, must ensure that all 20 records reflect accurate contact information. This level of granularity can be easy to overlook for organizations that manage CLIA compliance centrally but operate across distributed physical locations.
Who Is Most at Risk of Non-Compliance
The paperless transition, while operationally straightforward for well-resourced organizations, introduces meaningful compliance risk for several categories of providers.
Small and independent physician office laboratories represent the largest at-risk cohort. According to CMS data, physician office laboratories account for approximately 122,000 of the more than 317,000 CLIA-certified entities — roughly 38% of the total universe. Many of these operate without dedicated compliance or administrative staff. The physician-owner or office manager who handles CLIA matters may be unaware of the March 1 deadline, may have an outdated email address on file with the State Agency, or may not have received the various outreach communications CMS and partner organizations have distributed over the preceding months.
Long-term care facilities present a related challenge. According to the American Health Care Association and NCAL, most nursing homes hold CLIA certificates — typically Certificates of Waiver for point-of-care testing — and the administrative staff responsible for managing those certificates may experience significant turnover. A nursing home whose CLIA contact information reflects a former director of nursing or a past administrator faces real risk of missed communications after March 1.
Rural and safety-net providers also warrant particular attention. Federally Qualified Health Centers, rural health clinics, and critical access hospitals often operate in resource-constrained environments with limited administrative bandwidth. Many have historically relied on paper communications precisely because their administrative workflows were built around physical documents. Transitioning to electronic systems requires not just updating a contact record but potentially rebuilding the organizational habits and processes through which CLIA-related communications are received, routed, and acted upon.
Multi-site health systems face a different kind of risk — one of scale and data management. A large integrated delivery system may hold dozens or even hundreds of CLIA certificates across its laboratory network, spanning hospitals, outpatient surgery centers, urgent care facilities, and physician office practices. Ensuring that every certificate record reflects an accurate, monitored email address requires a systematic audit of the entire CLIA portfolio — a task that, while manageable for organizations with robust compliance infrastructure, requires deliberate effort and coordination.
Operational Implications: Beyond the Immediate Deadline
While the most immediate concern is meeting the March 1 deadline, the paperless transition carries longer-term operational implications that warrant strategic attention.
For revenue cycle management, the connection between CLIA certification status and claims payment is direct. Medicare and Medicaid claims for laboratory services require a valid, current CLIA number. A claim submitted without a valid CLIA number — or with one associated with a lapsed or suspended certificate — will be denied. If a laboratory fails to receive its renewal fee coupon because the email on file is outdated, misses the billing deadline, and allows its certificate to lapse, the path from an administrative oversight to a reimbursement disruption is short.
The financial exposure is concrete. CLIA certification fees range from $150 for a Certificate of Waiver to $5,482 for the largest high-complexity laboratories — modest amounts that, if missed due to a failed electronic notice, could trigger a certificate lapse carrying far larger consequences. A mid-size physician group laboratory billing approximately $2 million annually in Medicare Part B claims faces a potential 100% revenue interruption for any period in which its CLIA certificate is suspended. For long-term care facilities operating on thin margins, even a two-week billing gap during a lapse resolution process could represent a material cash flow event. On the federal side, eliminating paper printing and mailing for 317,000+ certificate holders represents an estimated savings of several million dollars annually in program administration costs — a meaningful efficiency gain given the CLIA program’s self-funded fee structure. Revenue cycle teams should therefore incorporate CLIA certificate expiration monitoring into standard billing compliance workflows, independent of whatever the laboratory receives or does not receive from CMS.
For compliance and risk management functions, the transition underscores the importance of maintaining a current, audited registry of all CLIA certificates held by the organization, the email addresses associated with each, the certificate expiration dates, and the renewal timelines. This kind of registry serves not only as a tool for managing the paperless transition but as a foundation for ongoing CLIA compliance hygiene — a domain that receives insufficient administrative attention in many organizations until something goes wrong.
For healthcare associations, accreditation organizations, and State Agencies, the transition creates an outreach imperative. CMS has published a partner toolkit with ready-to-use messaging for disseminating information about the transition. Organizations that interact with CLIA-certified laboratories in any capacity — professional associations, group purchasing organizations, billing services, healthcare management companies — have a role to play in ensuring that the laboratories they serve have completed the transition steps before the deadline.
The Broader Context: Modernizing Federal Laboratory Oversight
Viewed in broader perspective, the CMS/CLIA paperless transition reflects a larger trend toward digital modernization of federal healthcare program administration — and carries implications beyond the immediate operational change.
The CLIA program has in many respects remained administratively static for decades. The core regulatory framework was established by the Clinical Laboratory Improvement Amendments of 1988, and while the substantive standards have been updated over time, the administrative infrastructure supporting the program — paper certificates, mailed fee coupons, phone-based inquiries — has changed comparatively little. The paperless transition represents a meaningful modernization of that infrastructure, one that aligns the CLIA program with the digital capabilities that most healthcare organizations already use for other administrative functions.
There are potential longer-term benefits beyond operational efficiency. An electronic communication system creates a more reliable and auditable record of certificate issuance and renewal notices. It enables CMS and State Agencies to push targeted program updates more efficiently. It reduces administrative costs associated with printing and mailing physical documents at scale across a universe of more than 300,000 laboratories. And it establishes the digital infrastructure through which future CLIA program improvements — such as online certificate amendment processes or real-time compliance dashboards — might eventually be built.
For laboratories and health systems, embracing the transition as an opportunity rather than a burden means using the March 1 deadline as a catalyst for a broader audit of CLIA compliance records, contact information, renewal timelines, and administrative workflows. Organizations that treat this as a one-time checkbox exercise — update an email address and move on — may find themselves underprepared for future regulatory changes that assume a functional digital communications channel between CMS and certified laboratories.
***
The CMS/CLIA transition to electronic-only communications, effective March 1, 2026, is one of the most consequential administrative changes to affect the laboratory compliance landscape in years. It touches every one of the more than 317,000 certified laboratory facilities in the United States — from the largest reference laboratories to the smallest physician office point-of-care testing site. The compliance steps required are clear and manageable, but the window for completing them is narrow, and the consequences of missing the deadline — lapsed certificates, undelivered fee coupons, disrupted reimbursement — are operationally and financially serious.
For laboratory directors, compliance officers, revenue cycle managers, and healthcare executives, the message is unambiguous: confirm that CMS has a current, monitored email address on file for every CLIA certificate your organization holds, update the CMS-116 form accordingly, and build the organizational processes to monitor electronic CLIA communications going forward. The era of paper certificates is ending. The organizations that treat this transition as a strategic opportunity to modernize their laboratory compliance infrastructure will be better positioned not only for March 2026 but for the ongoing evolution of federal laboratory oversight in the years ahead.
If you enjoyed this piece, subscribe to our monthly newsletter to receive even more in-depth insights.
Sources
- Centers for Medicare & Medicaid Services. (2025). Clinical Laboratory Improvement Amendments (CLIA) — Transition to Paperless. https://www.cms.gov/medicare/quality/clinical-laboratory-improvement-amendments
- Centers for Medicare & Medicaid Services. (2025). CLIA Partner Toolkit Fact Sheet: Changes to CLIA Fees & Certificates. https://www.cms.gov/files/document/clia-partner-toolkit-fact-sheet.pdf
- Centers for Medicare & Medicaid Services. (2025). CLIA Transition to Paperless Toolkit. https://www.cms.gov/files/document/clia-transition-paperless-toolkit.pdf
- Centers for Medicare & Medicaid Services. (2024, March). CLIA Statistics Database — March 2024. https://www.cms.gov/regulations-and-guidance/legislation/clia/downloads/statupda.pdf
- Centers for Medicare & Medicaid Services. (2025). CLIA Fee Schedule. https://www.cms.gov/regulations-and-guidance/legislation/clia/clia_fee_information
- American Health Care Association / National Center for Assisted Living (AHCA/NCAL). (2025). The CLIA Program is Making the Switch to Paperless by March 2026. https://www.ahcancal.org/News-and-Communications/Blog/Pages/The-CLIA-Program-is-Making-the-Switch-to-Paperless-by-March-2026.aspx
- LeadingAge. (2025, August 13). CLIA Goes Paperless March 1, 2026. https://leadingage.org/clia-goes-paperless-march-1-2026/
- Laboratory Economics. (2025, July 24). CLIA Database of 321,000+ Labs. https://www.laboratoryeconomics.com/product/clia-database/
- Carey, R. B., et al. (2024). Estimation of Numbers of Testing Personnel and Test Volume in the CLIA Certificate of Accreditation and Certificate of Compliance Laboratories in the United States. PMC / National Library of Medicine. https://pmc.ncbi.nlm.nih.gov/articles/PMC11024983/
Discover more from Doctor Trusted
Subscribe to get the latest posts sent to your email.
