Clinical laboratories in the U.S. operate within a complex regulatory system that monitors the accuracy and quality of testing. Laboratories must be familiar with the regulatory process and the agencies that inspect and accredit laboratories in order to meet quality guidelines, maintain inspection readiness, and ensure their staff understand and follow policies.

The Centers for Medicare and Medicaid Services (CMS) sets standards and regulates all clinical laboratory testing performed on patients in the U.S. through the CLIA. CLIA, which applies to approximately 260,000 laboratory entities, covers laboratory operations and the performance of both laboratory-developed tests (LDT) and Food and Drug Administration (FDA)-cleared or approved tests marketed by in vitro diagnostic (IVD) manufacturers. The Division of Laboratory Services, within the Survey and Certification Group, under the Center for Clinical Standards and Quality, has the responsibility for implementing the CLIA program.

Before they can accept human samples for diagnostic testing, clinical laboratories must obtain a CLIA certificate through their state agency and be accredited by CMS or a CMS-deemed organization, such as the College of American Pathologists (CAP). The states of Washington and New York operate differently, with their own agencies that regulate laboratory testing, including certification and inspection programs.

The CLIA program is 100% user-fee financed and jointly administered by three agencies within the Department of Health and Human Services—FDA, CMS, and the Centers for Disease Control and Prevention (CDC). Each agency has a unique role in assuring quality laboratory testing (Table 1). CLIA compliance is essential for getting reimbursement from federally funded programs such as Medicare and Medicaid and other insurance agencies.

Laboratories can obtain multiple types of CLIA certificates based on the kinds of testing they perform, including point-of-care testing (POCT), provider-performed microscopy (PPM), moderate complexity, and high complexity. Under CLIA regulations, when a laboratory uses a test system that has not been approved by FDA, such as a LDT, this is considered high complexity testing. A laboratory may not release any test results prior to establishing a test’s analytical validity.

Accreditation Organizations

Currently, seven independent accreditation organizations may certify clinical laboratories under CLIA. These deemed agencies make sure that laboratories follow CLIA regulations but may also enhance requirements beyond what CLIA stipulates. CMS is responsible for overseeing criteria for accrediting agencies that work on behalf of the agency. CMS does not regularly inspect laboratories accredited under a deemed organization in good standing but can still inspect unannounced at any time.

For example, CMS recognizes CAP guidelines and inspections as equivalent to or more stringent than CLIA requirements. CAP requirement checklists at minimum encompass all CLIA standards. However, deemed agencies have guidelines, checklist items, and processes of inspection that can differ substantially from each other. For example, CAP conducts lab inspections with the help of volunteers from other CAP-accredited peer laboratories, whereas full-time staff of COLA (formerly the Commission on Office Laboratory Accreditation) and The Joint Commission (TJC) perform inspections for these organizations.

Types of CMS Deficiencies

CMS deficiencies fall into two general categories. Standard level deficiencies describe a laboratory’s failure to follow an individual requirement in CLIA regulations. Condition level deficiencies are more serious and may involve failure on multiple standards. Further, CMS defines deficiencies as having no immediate jeopardy or immediate jeopardy, with the latter the most serious. Deficiencies in the immediate jeopardy category indicate that a laboratory’s noncompliance already has or could lead to serious patient harm or death.

One example of a condition level deficiency that CMS considers especially serious is proficiency testing referral, which occurs when a surveyor determines that a laboratory has intentionally referred proficiency testing to another laboratory. This results in a mandatory citation even if there is not documented negative outcome or potential harm.

Top Deficiencies Found by CMS Surveyors

As of January 2018, CMS was responsible for surveying 17,967 laboratories. This number does not include nearly 12,000 physician office laboratories, nor the 184,298 laboratories that perform waived testing and are exempt from inspection and most other CLIA requirements.

Common standard level deficiencies in laboratories inspected by CMS include: testing personnel competency assessment, reagent storage according to manufacturer’s instructions (includes humidity requirements), use of expired reagents, improper instrument maintenance records, and analytical measurement range verification. Documentation of acceptable specimen criteria, proper patient identification, and checks for quality in analytical systems also make the top 10 list (See Table 2).

Of the more serious condition level deficiencies, problems with personnel requirements and qualifications predominate (six out of 10 top citations). Personnel deficiencies relate to qualification requirements of the laboratory director, technical consultant, laboratory supervisor, and testing personnel.

Laboratories should create a process to verify their job descriptions against CLIA standards and ensure that all staff serve in one of the CLIA-defined roles with appropriately documented education, training, and experience. These requirements should also be incorporated into the hiring process as labs screen applicants.

Proper proficiency testing procedures and maintaining and monitoring lab equipment are the next major condition level deficiencies. The total number of condition deficiencies
significantly smaller than standard level deficiencies—CMS cited 878 (5.1%) of labs surveyed for the number one standard level deficiency versus 465 (2.6%) of labs surveyed for the top condition level deficiency.

Comparing Common Deficiencies

Reviewing the deficiency lists from TJC, CAP, COLA, and CMS, common problems emerge. Laboratories can be better prepared for inspections—and increase their attention to essential quality systems—by focusing efforts in these areas since so many struggle to meet standards.

The most common areas of deficiencies among all the agencies include: testing personnel qualifications and competency evaluation, proficiency testing, method comparisons and analytical measurement range (AMR) verification, and instrument maintenance and service visit documentation.

College of American Pathologists

Competency assessment of testing personnel led the list of CAP deficiencies for 2016, followed by instrument correlations/method comparisons, review of procedure manuals by the lab staff and medical director, evaluation of proficiency testing results, and review of equipment function checks/maintenance records. Proper reagent labeling, updating activity menu, and documentation of method validation also resulted in a significant number of deficiencies (See Table).


COLA’s top 10 deficiencies in 2016 primarily include not fulfilling personnel responsibilities. Examples of specific problems include lack of review of quality control, proficiency testing results not reviewed by the laboratory director, and issues with defining technical consultant and lab supervisor roles and responsibilities (See Table).

The Joint Commission

TJC standards emphasize the results a laboratory should achieve, not the specific methods of compliance, and were developed with input from professional laboratory organizations. TJC top 10 deficiencies in 2016 include testing personnel competency evaluation, instrument correlations, proficiency testing participation, instrument maintenance records, AMR verification, and individualized quality control plans for waived testing (See Table).

Responding to Deficiencies

If cited, a clinical laboratory must submit a written response within 10 business days of receiving a CMS statement of deficiencies. This response is known as the plan of correction (form CMS-2567). An acceptable plan of correction addresses all deficiencies noted and must be specific, realistic, and complete. The plan also must name the individual responsible for monitoring the corrective actions and note the date of completion for each citation. The laboratory must reach compliance under the plan and be prepared for a follow-up visit within 30-45 days from the date of the original survey.

Importantly, the laboratory must complete a plan of correction and provide acceptable evidence that the deficient practices have been rectified before the condition is considered in compliance.

Becoming Inspection-Ready

Laboratory directors and other leaders are responsible for ensuring that their laboratories are inspection-ready at all times. While a particular person on staff may be designated to coordinate accreditation and inspection activities, all employees need to understand their roles and responsibilities. Regulatory compliance is the responsibility of every individual that works in a laboratory.

Leaders must involve the entire staff in all levels of inspection readiness—which should be part of everyday decision-making. Decisions about staffing, equipment, reagents, controls, and other aspects of lab operations should consider the effect on a laboratory’s inspection readiness.

Carrying out a self-inspection is a good place to begin to determine whether a laboratory is compliant with CLIA regulations. Any deficiencies found—during either a mock or a real inspection—should be addressed as individual line items as well as assessed as a group to determine if the laboratory has a systemic problem.

Quality programs are not extras: They ensure the robustness of the overall performance of a clinical laboratory. By performing self-inspections and dealing with any problems, laboratories improve staff morale, preserve the organization’s reputation, and avoid costly citations.


Understanding regulations and guidelines from CMS and accreditation agencies helps make a successful quality lab. A laboratory’s management should emphasize a culture of continual inspection readiness, addressing problems as soon as they are identified.

It’s no secret that regulations and guidelines are often not easy to understand, especially as they relate to a laboratory’s specific testing needs. When in doubt, a laboratory should always contact its accrediting agency with questions. Laboratory compliance is an ongoing process, and every member of the lab team a key stakeholder.


  1. Centers for Medicare and Medicaid Services. CLIA top ten deficiencies in the nation. (Accessed June 2018).
  2. College of American Pathologists. List provided by Senior Director, Accreditation and Regulatory Affairs.
  3. COLA. List provided by Kathy Nucifora, Director of Accreditation.
  4. The Joint Commission Perspectives 2017;37(4).
  5. Eden PR, Davis CM, and Herring CF. Getting ready for your laboratory inspection. (Accessed June 2018).
  6. Centers for Medicare and Medicaid Services. State operations manual appendix C – survey procedures and interpretive guidelines for laboratories and laboratory services. (Accessed June 2018).
  7. Ehrmeyer SS, Laessig RH. Has compliance with CLIA requirements really improved quality in U.S. clinical laboratories? Clin Chim Acta 2004;346:37-43.
  8. Centers for Medicare and MedicaidServices. CLIA program and Medicare laboratory services. (Accessed June 2018).
  9. Centers for Medicare and Medicaid Services. Personnel policies for individuals directing or performing non-waived tests. (Accessed June 2018).
  10. Centers for Medicare and Medicaid Services. CLIA update – January 2018. (Accessed June 2018).

Seetharam Chittiprol, PhD, DABCC is the technical director of clinical chemistry at Pathology Consultants of South Broward, Memorial Healthcare System, in Hollywood, Florida.+Email: seetha0109[at]

Joshua A Bornhorst, PhD, DABCC, FADLM, is the associate director of the clinical immunoassay and metals testing laboratory at Mayo Clinic in Rochester, Minnesota.+Email: bornhorst.joshua[at]

Frederick Kiechle, MD, PhD, FADLM, is a consultant pathologist in Cooper City, Florida.+Email: fkiechle[at]