CLIA inspection deficiencies—what they mean and how to avoid them

Sept. 1, 2012

A common question posed by laboratorians is, “How do I avoid CLIA inspection deficiencies?” A closely linked question is, “What do CLIA inspection deficiencies mean?” One way to answer both questions may be to look at what the most common citations are, and then audit your facility for compliance.

The best way to assess overall compliance with the CLIA regulations is to conduct a mock inspection. This may be performed internally, or more appropriately, by a third party. Checklists for mock CLIA inspections can be located on the web. Useful websites to consult include; and

In the last several years, consultants, organizations, and newsletters on the web have noted an increasing trend of rigorous CLIA inspections. While deficiencies in general are discussed below, I will first address two specific areas that have repeatedly been in the spotlight: staff qualifications and proficiency testing.

Staff qualifications

The regulatory requirements for staff are clearly defined in 42 CFR 493, and are described based on testing complexity (high and moderate). Text complexity classifications may be located on the FDA website at Staff must be qualified at the level of the highest complexity assay your laboratory performs. There are also several things to consider with regard to test complexity and staff qualifications. It is important to check the test complexity database when implementing new technology or when changing assays for a given analyte (or analytes). Some analytes have assays with different levels of complexity. Automated hemoglobin and glucose are two examples of this; both have waived assays and moderate-complexity assays. Should you be testing using an analyte-specific waived assay and change to a moderate-complexity assay for the same analyte, or if your laboratory only performs waived testing and implements testing with moderate-complexity assays, you must ensure that all levels of staff for moderate-complexity testing (including directors) are qualified. The same applies for change to or implementation of high-complexity assays.

Inadequate staff qualification is not an infrequently cited deficiency, particularly for individuals in supervisory positions. The Laboratory Director, Technical Consultant, or Clinical Consultant must meet the regulatory qualifications (both for CLIA and your state), including having appropriate degrees, licenses, CMEs, laboratory training, and/or laboratory experience. When individuals take CLIA specific courses, these courses are not replacements for the laboratory training or experience requirements. There is a common misconception that CMEs are acceptable as a replacement for laboratory training or experience.

Proficiency testing (PT)

Another recent area of concern is the submission of PT specimens to other laboratories for testing. 41 CFR 483.801 (4) states: “The laboratory must not send PT samples or portions of samples to another laboratory for any analysis which it is certified to perform in its own laboratory. Any laboratory that CMS determines intentionally referred its proficiency testing samples to another laboratory for analysis will have its certification revoked for at least one year.” Intuitively, this makes sense. However, if your laboratory performs testing but sends samples to another laboratory for additional or confirmatory testing, sending PT samples to that other laboratory is considered intentional PT referral and may result in the same certification revocation. Therefore, on your PT documentation you should indicate “Not applicable” for the additional or confirmatory testing.

Other common deficiencies found are failure to rotate PT to include all personnel who perform the test; failure to retain the records, reports, and attestation statements for two years; failure to take and document corrective action when unsatisfactory proficiency testing has occurred; and failure to verify the accuracy of non-regulated tests at least twice annually.


In order to ensure CLIA compliance, it is important to read and review the CLIA regulations. Because they are guidelines, they may be misunderstood, or they may not be clear as they relate to your specific laboratory. The Interpretive Guidelines are a good reference for more detailed explanation of a given regulation and are located at The State Operations Manual (Chapter 6, Special Procedures for Laboratories; Sections 6000 – 6139 Program Background and Actions Related to Certification) is a good reference for certification, survey, and CLIA action information. It is located at

Unanswered questions should be directed to your state or regional CLIA contact, who may be located at

Below is a list of the nation’s top 10 CLIA deficiencies in 2008, their rankings, d-tag number, regulation citation, and short description of the deficiency:

  • D5413 §493.1252 Standard: Test systems, equipment, instruments, reagents, materials, supplies. The laboratory must define criteria for those conditions that are essential for proper storage of specimens and reagents, accurate and reliable test system operation, and test result reporting. These conditions must be monitored and documented. Poor storage of reagents.
  • D5217 §493.1283 Standard: Evaluation of proficiency testing performance. For those tests not listed subpart I (not regulated), the laboratory must verify the accuracy of the test or procedure at least twice annually. Lack of proficiency testing.
  • D5791 §493.1299 Standard: Postanalytic systems quality assessment. The laboratory must establish and follow written policies and procedures for an ongoing quality assessment (QA) plan to monitor and assess the requirements of Analytic System, as well as the corrective action process when problems or potential problems are identified. No quality assessment program.D5411 §493.1252 Standard: Test systems, equipment, instruments, reagents, materials, supplies. Test systems must be selected by the laboratory. The testing must be performed following the manufacturer’s instructions and in a manner that provides test results within the laboratory’s stated performance specifications. Directions not followed; equipment maintenance/calibration not performed per manufacturer’s directions.
  • D5403 §493.1283 Standard: Procedure manual. Requirements to include that are applicable to a test procedure. Incomplete procedure manual.
  • D5291 §493.1239 Standard: General systems quality assessment. The laboratory must establish and follow written policies and procedures for an ongoing quality assessment (QA) plan to monitor and assess the requirements of General System, as well as the corrective action process when problems or potential problems are identified. No quality assessment program.
  • D6021 §493.1407 Standard: Laboratory director responsibilities. The laboratory director must ensure quality assessment programs are established and maintained to assure the quality of laboratory services provided. Director not requiring a quality assessment program, or not adhering to an existing quality assessment program.
  • D5417 §493.1403 Condition: Laboratories Performing Moderate Complexity Testing; Laboratory Director. The laboratory must have a director who meets the qualification requirements of §493.1405 of this subpart and provides overall management and direction in accordance with §493.1407 of this subpart. Inadequate qualifications and/or not fulfilling responsibilities.
  • D5805 §493.1283 Standard: Test report. Requirements for information provided in a test report not complete or missing test reports.
  • D6000 §493.1252(d): Reagents, solutions, culture media, control materials, calibration materials, and other supplies must not be used when they have exceeded their expiration date, have deteriorated, or are of substandard quality. Expired reagents used.

Full d-tag descriptions are described in the State Operations Manual, Appendix C—Survey Procedures and Interpretive Guidelines for Laboratories and Laboratory Services, located at

Deficiency assessment can be discussed using the list above as an example. The deficiencies can be grouped into what might be considered “straightforward” deficiencies and “conceptual” deficiencies. The straightforward deficiencies are those that clearly can be corrected by improving or implementing a process: appropriate storage criteria for, and/or use of, reagents; implementing accuracy/proficiency testing for subpart I tests; following the manufacturers’ directions; drafting complete procedures; including all required information on and/or retaining appropriate test reports; employing staff with appropriate qualifications. An example of a conceptual deficiency would be any of those associated with a Quality program, which is a system. In a time of lean staffing, Quality programs are often considered an extra or a luxury. Additionally, many people struggle with the concept of a Quality program, and how to implement it. The implementation of an appropriate Quality program may require external assistance or consultation.


Performing a mock inspection of your laboratory is a good place to begin to determine if you are compliant with the CLIA regulations. But deficiencies found here (or during a real CLIA inspection) should not only be reviewed and addressed as individual line items; they should also be assessed as a group to determine if your laboratory has a systemic problem. An assumption that Quality programs (or Quality elements) are extras or luxuries is incorrect; they ensure the robustness of the overall performance of your laboratory. Therefore, being successful requires that your establishment embrace a quality culture, from the testing staff up through senior management.

So what are the financial costs associated with complying with CLIA? What about the costs of CLIA inspection deficiencies? It may be hard to quantify the financial cost of ensuring compliance with CLIA. But it should not be hard for you, at your individual laboratory, to quantify the financial cost associated with CLIA certificate revocation resulting in loss of reimbursement, and/or, more seriously, a requirement to cease operations until compliance is achieved. Severe deficiencies that result in the loss of CLIA certification may also be accompanied by consequences not just for the laboratory owner, but also for the Medical Director, who may face suspension or revocation of his or her license for as long as two years. The cost to ensure compliance is outweighed by the risk of being found deficient, and the cost associated with certificate revocation. It is a necessity to avoid deficient laboratory performance and the associated cost to healthcare.

Sharyn Orton, MT(ASCP)SBB, MPSH, PhD, is Senior Consultant for Massachusetts-based MEDIcept, Inc.