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10 Top CLIA Deficiencies for Labs and How to Avoid Them

by | Jun 25, 2024 | CLIA-lca, Compliance Perspectives-lca, Essential, Lab Industry Advisor

Areas to address when preparing for your next CLIA inspection, based on recent data on top CLIA deficiencies

If you own or operate a diagnostic laboratory, you can expect to be inspected at least every other year by the local Clinical Laboratory Improvement Amendments of 1988 (CLIA) office that oversees your geographic area. Such inspections occur even if you have not introduced new testing or had any personnel changes. Though CLIA inspections aren’t usually a surprise, even well-established labs can be thrown for a loop by the inspection process or incur deficiencies when unprepared.

Which deficiencies are the most common? Lab leaders can find the top 10 list on the website of the U.S. Department of Health and Human Services (HHS) Centers for Medicare & Medicaid Services (CMS).1 Below is a brief explainer of these common CLIA deficiencies categorized by type, as well as tips for avoiding them:

Analytic systems deficiencies

Of 10 historically common deficiencies cited during CLIA inspections, four relate to analytic systems standards.1

Deficiency (493.1235): The analytic standard requiring laboratories to define the “conditions that are essential for proper storage of reagents and specimens, accurate and reliable test system operation, and test result reporting” was violated in 17.5 percent of recently inspected labs.

Solution: This deficiency can be corrected with minimal time and effort simply by developing clear standard operating procedures (SOPs) with definitions for all of these conditions. Such SOPs should be readily available to all lab personnel, and the inspector will review SOPs in depth during the inspection process.

Deficiency (493.1251(b)): Another common deficiency with regard to analytic standards concerns the procedure manual in the lab, which “must include the requirements for specimen acceptability, microscopic examination, step-by-step performance of the procedure, preparation of materials for testing, etc.”

Solution: Having a dedicated procedural manual binder in the lab with physical copies of all SOPs and/or a digital copy that is available to staff and the inspector can help you avoid this deficiency.

Deficiency (493.1254(a)(1)): Insufficient maintenance is another frequent issue, with just over 13 percent of recently surveyed labs not performing maintenance on lab equipment at the frequency mandated by the manufacturer.

Solution: Having a staff shared calendar noting when each piece of equipment and instrumentation needs regular maintenance, and documenting said maintenance alongside the related SOPs is a straightforward way to avoid citations for lack of maintenance during an inspection.

Deficiency (493.1252(d)): Another common issue involving analytic standards concerns the use of consumables and supplies that are either expired, deteriorated, or of substandard quality. This includes reagents and other supplies used to test specimens, as well as control and calibration materials, etc.

Solution: It’s lab leadership’s responsibility to ensure that all supplies used in the laboratory are unexpired, have not deteriorated due to conditions in the lab or other causes, and are deemed of an acceptable quality by CMS and CLIA. Keeping a regular check on these supplies, including logging their expiration dates and related SOPs in the appropriate binders in the lab, is the best way for lab leaders to ensure compliance with this CLIA standard.

Personnel deficiencies

Deficiency (493.1235): Lab leaders may be surprised to learn that one of the most common deficiencies involves the completion of staff competency assessments. Nearly 19 percent of recently surveyed labs did not meet this standard, which concerns both the establishment and following of policies for such evaluation. Both lab employees and consultants who fulfill any CLIA personnel roles must have their competency evaluated regularly, as set forth in the CLIA standards.

Solution: Having an SOP for how each staff member’s specific role should be assessed, and keeping a schedule of when these assessments must occur on a shared calendar are two ways to meet this CLIA standard and avoid this particular deficiency. Otherwise, with various staff members hired at different times during the year, it can be difficult to keep up with competency evaluations and when staff need to be reassessed.

Deficiency (493.1407(e) (4)(i)): A second common personnel responsibility deficiency relates to the CLIA laboratory director’s duty to ensure the lab was enrolled in a proficiency testing program approved by HHS; just over 10 percent of labs recently received this citation.

Solution: Speaking with your current lab director and ensuring you are enrolled in appropriate proficiency testing is the easiest way to avoid this deficiency. Lab leaders can find a list of all HHS approved proficiency testing programs for 2024, organized by testing specialty, on the CMS website.2

Performance specification deficiencies

The final four deficiencies cited in recent inspections have been grouped together due to their common thread: specifications related to the systems and performance of the laboratory, including staff, instrumentation, etc.

Deficiency (493.1236(c)(1)): All tests performed in-house in a CLIA licensed laboratory must be assessed twice per year for accuracy. More than 16 percent of recently inspected labs received a deficiency for failure to do so.

Solution: Adding scheduled twice yearly accuracy assessments to the lab’s shared calendar can help ensure compliance.

Deficiency (493.1253(b)(1)): Any test or procedure that is unmodified from the manufacturer and/or is FDA-approved or cleared must be demonstrated, during inspection, to have performance specifications comparable to those established by the manufacturer. Nearly 16 percent of recently inspected labs failed to do so.

Solution: To ensure compliance with this standard, keeping those specifications in the appropriate SOPs is paramount. Before the inspection, labs may also wish to test performance to ensure it is within the appropriate range.

Deficiency (493.1251(a)): More than 14.5 percent of recently inspected labs either failed to have documented written procedures for “all tests, assays, and examinations performed by the laboratory” or their staff failed to follow said procedures during inspection. Because this is either a failure of lab management to have documented procedures or negligence of staff to follow established procedures, it is lumped in with the other performance deficiencies.

Solution: The key to avoiding multiple citations is to establish policies and written procedures, and ensure these are in place and followed by staff ahead of inspection.

Deficiency (493.1291(c)): Violations related to test report requirements are another common issue found during CLIA lab inspections. The post analytic systems standard—493.1291(c)—mandates that, “The test report must indicate the following: for positive patient identification, either the patient’s name and identification number, or a unique patient identifier and identification number, the name and address of the laboratory location where the test was performed, and other requirements specified in 493.1291(c).”

Solution: Reviewing the lab’s test report form in comparison to the requirements provided in 493.1291(c) can help ensure all necessary information has been included and the lab is compliant.3

Are you prepared for your next CLIA inspection?

If that question scares you a little, don’t fret. Following the advice detailed here, alongside that in our accompanying Compliance Tool, can help you avoid the most commonly occurring deficiencies. The two main recommendations to avoid these citations include creating a shared calendar with important dates on it and readying your personnel and procedural documentation. Just having your paperwork in order can help you avoid many recent CMS reported deficiencies.

According to Rahul Nahire, PhD, a CLIA consultant and certified quality auditor with more than 14 years of experience as a CLIA laboratory director, the best thing lab leaders can do to ensure ongoing compliance is to develop and implement a monthly quality assurance (QA) program. A QA program ensures that many of the basic activities suggested here are checked regularly. Having a short checklist that your lab manager or director can run through each month can be a quick way to maintain compliance and avoid needing big overhauls when preparing for inspection. Such a program also helps ensure problems are identified as early as possible so lab leaders have plenty of time before the inspection to address any issues.

Performing a mock audit ahead of inspection can also ensure preparedness and helps identify any areas of concern, allowing for correction prior to the formal CLIA audit. In general, simply keeping CLIA standards top of mind can go a long way toward maintaining overall compliance.


    1. https://www.cms.gov/Regulations-and-Guidance/Legislation/CLIA/downloads/CLIAtopten.pdf

    1. https://www.cms.gov/Regulations-and-Guidance/Legislation/CLIA/downloads/ptlist.pdf

    1. https://www.govinfo.gov/content/pkg/CFR-2011-title42-vol5/pdf/CFR-2011-title42-vol5-sec493-1291.pdf

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