Tools, Technologies and Training for Healthcare Laboratories

CLIA Final Rule

Part VIII: The Interpretive Guidelines

CLIA Interpretive Guidelines:
Appendix C of the State Operations Manual

On January 12, 2004, CMS released Appendix C of the State Operations Manual. That happens to be the Interpretive Guidelines for the CLIA Final Rule. And what is contained in those interpretations are some major changes in how laboratories will be regulated, and what kind of QC they will be allowed or required to perform. Get the first look at the true impact of these guidelines with the help of Dr. Sharon Ehrmeyer, Ph.D. and Dr. Westgard

January 2004

Most of us have questions about the meaning and interpretation of the CLIA rules and regulations. To address these issues, CMS has published “interpretive guidelines” that are available on the Internet [1,]. Given that these guidelines were just published on January 12, 2004, many of us also have questions about the meaning and interpretation of the new interpretative guidelines.

The interpretive guidelines are technically identified as Appendix C of the State Operations Manual (SOM, CMS Publication 7), a manual used by states in administering various federal programs, not just CLIA. However, these updated Interpretive Guidelines have a new twist in that they have become a companion to the final CLIA Rule [2]. In the past, surveyors primarily used the probes listed in the Guidelines during the inspection process to determine a laboratory’s compliance with a particular standard. Now the document is being made available to laboratories to help them better understand the CLIA requirements and also to provide additional regulatory information not included in the Final Rule. For example, section §493.1256(d), Standard Control procedures, states: “Unless CMS approves a procedure, specified in Appendix C of the State Operations Manual, that provides ‘equivalent quality testing,’ the laboratory must…” follow the rules found in §493.1256 of the Federal Register [page 3707-8, reference 2]. The information on “equivalent quality testing” is found only in the SOM.


Appendix C includes 7 sections that are available as Portable Document Files (PDF) that can be downloaded to your computer or printed directly. The PDF format requires that you have the Adobe Acrobat Reader installed on your computer (which is available free and can be downloaded from the Adobe website

  1. Policy for conducting surveys (18 pages)
  2. Index and Subparts A-H. General Provisions, Certificates and Proficiency Testing: §493.1100 – §493.865 (59 pages)
  3. Subpart J. Facility Administration: §493.1100 – §493.1105 (11 pages)
  4. Subpart K, Part 1. Quality System for Nonwaived Testing; General Laboratory systems, Preanalytic Systems & Analytic Systems - general requirements: §493.1200 – §493.1256 (59 pages)
  5. Subpart K, Part 2. Quality System for Nonwaived Testing; Analytic Systems – specialty and subspecialty requirements – and Postanalytic Systems: 493.1261 – 493.1495(77 pages)
  6. Subpart M. Personnel: §493.1351 – §493.1495 (61 pages)
  7. Subpart Q. Inspection: §493.1771 – §493.1780 (11 pages)

That’s a total of 296 pages of new materials to help you better understand the CLIA Final Rule and how it will be applied in laboratory inspections.

Format and content

Unlike the previous Appendix C that was organized in table format, the new version follows the format:

Deficiency “D-tag number”
CLIA standard
Interpretive Guidelines, and

Here’s an example for §493.1251(a) Standard: Procedure Manual.

§493.1251 Standard: Procedure Manual

(a) A written procedures manual for all tests, assays, and examinations performed by the laboratory must be available to, and followed by, laboratory personnel. Textbooks may supplement but not replace the laboratory’s written procedures for testing or examining specimens.

Interpretive Guidelines §493.1251(a):

Procedures may be organized in the form of manuals, stored in computers and/or card files. Use D5401, if the procedure manual lacks any of the applicable information as specified in §493.1251(b)(1)-(14). If the laboratory has procedures that are not used for test performance, but are used for reference purposes, they may be placed in a reference section. You need not review reference procedures unless problems are identified with patient test results.

Centers for Disease Control and Prevention (CDC) and Armed Forces Institute of Pathology (AFIP) manuals, manufacturer’s operating instructions, and package inserts, are acceptable provided the policies and procedures are available, and the methods in use are clearly indicated. If the laboratory modifies any procedure, the modification must be documented and verified/established as specified in §493.1253.

Probes §493.1251(a):

How does the laboratory ensure that personnel follow the procedures in the procedure manual? How are changes in procedures communicated to laboratory personnel? For competency issues, use D6030 or D6103 as applicable.”

All CLIA standards have a “D-tag” assigned. When a laboratory is found in noncompliance with a particular standard, the surveyor cites the associated “D” number rather that the specific standard.

The Interpretive Guidelines section is designed to provide more information to both the laboratory and surveyor on how to meet the particular requirement. For the procedure manual example, the surveyor also is informed to use a specific D-tag “D5410” when the test site omits required information and to review the laboratory’s reference procedures only when problems occur with patient test results.

The Probes section is included to assist the surveyor in determining whether the laboratory is in compliance with the standard. These probes are in the form of questions and, for the procedure manual example, the surveyor is told to investigate how the laboratory ensures personnel follow the procedures and also to identify what mechanism is used to inform testing personnel of changes in the manual. Obviously, it is useful for the laboratory to be familiar with the probes since the surveyor should be following these directions during the inspection.

While there will be a D-tag for each CLIA standard listed, not all standards are included in the Interpretive Guidelines and/or Probes sections.

Issues and Answers

How should you use these Guidelines if inspected by CMS?

If your laboratory is inspected for CLIA compliance, be very familiar with the Guidelines and use them as a companion document to the Final Rule.

  • The Interpretive Guidelines section will further clarify the intent of the standard and, perhaps, provide assistance on what documentation or what strategies should be included to meet the standard. With the procedure manual standard, the Guidelines state that procedures may be organized in the form of manuals, stored in computers and/or card files.
  • The Interpretive Guidelines are particularly important for further guidance on equivalent quality testing, section §493.1256(d).
  • The Probes provide some clues as to what the surveyor will want to find. Simply having a response to each probe can eliminate many potential inspection problems. For the procedure manual example, make sure mechanisms are in place to ensure that personnel follow the procedures and changes in the manual are communicated to laboratory personnel.

What if your laboratory is inspected by a professional accrediting organization?

CMS “deems” or approves certain professional accrediting organizations, such as the College of American Pathologists (CAP), the Joint Commission for Accreditation of Healthcare Organizations (JCAHO), and the Commission for Office Laboratory Accreditation (now called COLA), as having requirements as or more stringent than CLIA and therefore allows them to carry out laboratory inspections [3].

Inspections conducted by these government-approved accrediting organizations are based on the specific testing requirements of the particular organization. By meeting the accrediting organizations requirements, test sites, in essence, also are meeting the CLIA requirements.

In most cases each of these organizations’ issues their own test standards and provides information similar to what appears in the Interpretive Guidelines section of Appendix C, for example:

CAP’s Laboratory General Checklist item GEN.11742 asks [4]: “Is there evidence that problems identified by proficiency testing and alternative performance assessment have been recognized and corrected?”

  • Under the COMMENTARY for this standard clarification is provided: “There must be evidence that the laboratory solves problems identified through proficiency testing and alternative performance assessment (as appropriate). Documentation of corrective/preventive action is required.”

JCAHO’s standard QC.1.110 states [5]: “The laboratory ensures that quality control results meet its criteria for acceptability before it reports patient test results.” The ELEMENTS OF PERFORMANCE section for this standard provides insight into what the inspector will want to see: (1) For each area of the laboratory, defined criteria exist for evaluating the acceptability of control and calibration results. (2) Individual results are not reported unless these criteria are met.

Don’t the interpretative guidelines allow CLIA to change the rules published in the Federal Register?

That certainly appears to be the case. As we have discussed earlier on this website, the interpretative guidelines for “equivalent” QC procedures [6] deviate greatly from the requirements for appropriate QC procedures [7] stated in the Federal Register. The advantage of using the SOM to make these changes is that CMS minimizes the need to solicit public comments and, likewise, minimizes the need to defend these changes. In effect, the SOM gives CMS considerable flexibility in the way the CLIA rules are actually applied and enforced.

DO’s and DON’Ts

  • DO obtain a copy of Appendix C for your laboratory. You can decide whether to store that copy on your computer or to print a copy. One advantage of a printed copy is that its sheer size makes it evident there is a lot of direction being given to inspectors and it should also be obvious that the laboratory needs to pay attention to these materials. At a minimum, print the two sections on the Quality System for Nonwaived Testing, since these materials contain new information not available elsewhere.
  • DO read the appropriate interpretive guidelines and probes for clarification and guidance in addressing specific rules that you find critical or troublesome for your laboratory. The specific interpretive guidelines and probes given in the SOM should be helpful for formulating strategies, implementing plans, and preparing for inspection.
  • DON’T be constrained or limited by the SOM. Recognize that the CLIA rules are minimum requirements for quality management. To assure quality test results for your patients, it may require doing more than the minimums specified by CLIA.
  • DO what is right to manage quality – let that be the guiding principle, not the CLIA rules and the SOM interpretative guidelines.


  1. Appendix C of SOM, Regulations and Interpretive Guidelines for Laboratories and Laboratory Services,
  2. CLIA Final Rule (2002 codification of all previous rules (1992-2002). and CLIA Final Rule (January 24, 2003)
  3. Listing of government-approved accrediting organizations.
  4. CAP Laboratory Accreditation Checklists.These used to be free, but now CAP charges for them.
  5. JCAHO standards. Joint Commission on Accreditation of Healthcare Organizations, One Renaissance Blvd., Oakbrook Terrace, IL 60181
  6. Westgard JO. CLIA Final Rule: Equivalent Quality Control Practices.
  7. Westgard JO. CLIA Final Rule: Appropriate QC Procedures.
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