CLIA - Clinical Laboratory Improvement Amendments

Overview

The Clinical Laboratory Improvement Amendments (CLIA) of 1988 established quality standards for all laboratory testing performed on humans in the United States. CLIA is administered by the Centers for Medicare & Medicaid Services (CMS) in conjunction with the CDC and FDA.

Statute: Public Law 100-578, October 31, 1988
Regulations: 42 CFR Part 493
Administering Agency: CMS, with CDC and FDA collaboration

Who Must Comply

Laboratory Definition

A CLIA laboratory is any facility that examines human specimens for health assessment or disease diagnosis, treatment, or prevention.

Must Obtain CLIA Certificate:

• Hospital laboratories


• Physician office laboratories (POLs)


• Independent laboratories


• Nursing home laboratories


• Public health laboratories


• Blood banks (for infectious disease testing)


• Community health centers


• Ambulatory surgical centers


• Home health agencies


• Pharmacies performing testing


• Urgent care centers


• Any entity performing testing on human specimens

Exemptions:

• Research laboratories not reporting patient-specific results


• Forensic laboratories


• Laboratories certified under VFC (vaccine) program for certain limited testing

Company Size

CLIA applies to ALL laboratories performing testing on human specimens, regardless of:

• Number of employees


• Test volume


• Annual revenue


• Facility type

CLIA Certificate Types

There are FIVE types of CLIA certificates, all valid for 2 years:

1. Certificate of Waiver (CoW)

• For: Laboratories performing only waived tests


• Requirements: Minimal (follow manufacturer instructions)


• Application Fee: $180 (biennial)


• Waived Tests: Simple tests with low risk of error (e.g., dipstick urinalysis, blood glucose meters, pregnancy tests)


• FDA Waived Test List: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfClia/analyteswaived.cfm

2. Certificate for Provider-Performed Microscopy (PPM)

• For: Physicians, midwives, dentists performing specific microscopy procedures


• Tests Allowed: 11 specific procedures (wet mounts, KOH preps, pinworm exams, etc.)


• Application Fee: $200 (biennial)


• Requirements: Minimal, no routine inspections

3. Certificate of Registration

• For: New laboratories awaiting survey before Certificate of Compliance


• Duration: Valid until survey completed (usually within 12 months)


• Application Fee: Included in biennial fee


• Requirements: Must meet all CLIA requirements immediately

4. Certificate of Compliance

• For: Laboratories performing moderate/high complexity testing, inspected by CMS/state agency


• Biennial Fee: Based on test volume and complexity (ranges from $640 to $12,320+)


• Survey Required: Biennial onsite inspection


• Requirements: Full CLIA compliance (quality systems, PT, qualified personnel)

5. Certificate of Accreditation

• For: Laboratories accredited by CMS-approved organization


• Biennial Fee: Based on test volume (same as Certificate of Compliance)


• Survey: Conducted by accreditation organization (typically annual)


• Requirements: Full CLIA compliance + accreditation standards

CMS-Approved Accreditation Organizations (7 Total)

1. AABB (blood banks, transfusion services)


2. ASHI (histocompatibility, immunogenetics)


3. CAP (College of American Pathologists) - most common


4. COLA (physician office labs)


5. ACLASS (compliance)


6. The Joint Commission


7. ASCP (American Society for Clinical Pathology)

Test Complexity Categories

CLIA categorizes tests by complexity, which determines requirements:

Waived Tests

• Criteria: Simple, accurate, minimal risk of error


• Examples: Dipstick urinalysis, blood glucose meters, pregnancy tests, rapid strep


• Requirements: Follow manufacturer instructions, enroll in CLIA


• Personnel: No specific qualifications required

Moderate Complexity

• Criteria: More complex procedures, higher risk


• Examples: Automated chemistry, hematology, automated immunoassays


• Requirements: Quality systems, proficiency testing, qualified personnel, biennial surveys


• Personnel: Testing personnel require high school diploma + training

High Complexity

• Criteria: Most complex, highest risk


• Examples: Manual microbiology, flow cytometry, molecular diagnostics, cytogenetics


• Requirements: Same as moderate PLUS more stringent personnel requirements


• Personnel: Laboratory director must be MD, DO, or PhD

Key Requirements for Nonwaived Testing

1. Quality Systems (Subpart K)

12 Essential Quality System Elements:

1. Personnel


2. Equipment


3. Purchasing and inventory


4. Process management


5. Documents and records


6. Occurrence management (incident reporting)


7. Assessment (audits)


8. Process improvement


9. Customer service


10. Facilities and safety


11. Proficiency testing


12. Comparability/verification procedures

2. Quality Control (Subpart K Sec.493.1256)

Traditional QC:

• At least two levels of controls daily


• Control ranges established and documented


• Corrective action when out of range


• Documentation of QC results

IQCP (Individualized Quality Control Plan) - Alternative:

• Risk assessment


• Quality control plan


• Quality assessment


• Must be equivalent to traditional QC

3. Proficiency Testing (Subpart H)

Requirements:

• Participate in CMS-approved PT program


• Test at least 5 samples three times per year (for each regulated analyte/test)


• Achieve 80% score in each event


• Testing personnel must not know PT samples


• No referral of PT samples allowed

PT Failure Consequences:

• First failure: Corrective action plan required


• Two consecutive failures or two out of three: Attestation required


• Three consecutive or three out of four: Sanctions imposed

CMS-Approved PT Programs:

• CAP Surveys


• COLA PT Program


• AABB PT Program


• AAB PT Program

4. Personnel Requirements (Subpart M)

Laboratory Director (High Complexity):

• MD, DO, or PhD with board certification or experience


• Responsible for overall operation and administration

Clinical Consultant (Moderate Complexity):

• MD, DO, PhD, or qualified Clinical Laboratory Scientist


• Provides interpretation and consultation

Technical Consultant:

• Minimum: Bachelor's degree in chemical/physical/biological science + 2 years experience

Testing Personnel:

• Moderate complexity: High school diploma + training


• High complexity: Associate degree or equivalent

Survey and Inspection Process

Inspection Frequency

• Nonwaived laboratories: Biennial (every 2 years)


• Accredited laboratories: Annual by accreditation organization


• Complaint-driven surveys: As needed


• Validation surveys: CMS oversight of accredited labs (10% annually)

Survey Components

1. Personnel qualification review


2. Quality control documentation review


3. Proficiency testing review


4. Equipment maintenance and calibration


5. Test performance observation


6. Procedure manual review


7. Facility inspection

Deficiency Categories

• Condition-level: Serious, may result in certificate sanctions


• Standard-level: Less serious, corrective action required


• Plan of correction: Required response within 10 calendar days

Enforcement and Penalties

Principal Sanctions

• Revocation: Certificate permanently cancelled


• Suspension: Certificate temporarily invalid (up to 1 year)


• Limitation: Restrict services (e.g., prohibit certain tests)

Alternative Sanctions

• Directed plan of correction: CMS-mandated corrective action


• On-site monitoring: CMS monitor on premises


• Civil money penalty: ~$2,000-$10,000+ per day per violation


• Refusal to renew: Certificate not renewed at expiration

Common Violations

• PT referral or collaboration


• Inadequate quality control


• Unqualified personnel


• Failure to maintain proficiency testing records


• Inadequate procedure manuals


• Failure to follow manufacturer instructions (waived tests)

Application Process

Steps to Obtain CLIA Certificate

1. Complete CMS Form 116 (Application for CLIA Certification)

• Download: https://www.cms.gov/Medicare/CMS-Forms/CMS-Forms/Downloads/CMS116.pdf


• Information Required: Laboratory name, address, director information, test menu, certificate type

2. Pay Application Fee

• Payment Methods: Check, money order payable to "CMS"


• Fees (2024):

- Certificate of Waiver: $180 (biennial)
- PPM Certificate: $200 (biennial)
- Certificate of Compliance/Accreditation: $640-$12,320+ (based on volume)

3. Submit Application

• Mail to: Your state agency (varies by state)


• Massachusetts: Division of Health Care Facility Licensure and Certification


• Processing Time: 4-8 weeks

4. Receive Certificate

• Certificate valid for 2 years from issue date


• Must be posted in laboratory

5. Renewal

• CMS sends renewal notice ~6 months before expiration


• Submit renewal application and fee


• Certificate remains valid during renewal processing

Massachusetts-Specific Requirements

Dual Licensure Requirement (for Nonwaived Testing)

Federal: CLIA Certification from CMS
State: Massachusetts Laboratory License from DPH

Massachusetts State Agency

Division of Health Care Facility Licensure and Certification

• Contact: [email protected]


• Phone: (617) 660-5385


• Address: 67 Forest Street, Marlborough, MA 01752

Massachusetts License Requirements

Application: https://www.mass.gov/how-to/apply-for-a-clinical-laboratory-license

State Fee: $300 per specialty area

Specialties:

• Clinical Chemistry


• Hematology


• Immunohematology (Blood Bank)


• Microbiology


• Immunology


• Cytology


• Etc.

State Survey: Required before license issuance (in addition to federal survey)

Important Change: As of 2022, laboratories performing ONLY waived testing no longer require Massachusetts state licensure (federal CLIA Certificate of Waiver sufficient)

Regional Considerations

• Massachusetts has numerous hospital laboratories, academic medical centers, and independent labs


• High concentration of specialty testing (molecular diagnostics, genetics, flow cytometry)


• State collaborates with CMS on survey activities

Compliance Implementation Timeline

Immediate (Before Testing)

• Enroll in CLIA (obtain certificate)


• Establish testing personnel qualifications


• Obtain necessary equipment


• Develop or obtain procedure manuals

Within 30 Days

• Enroll in proficiency testing programs (if nonwaived)


• Implement quality control procedures


• Train personnel on CLIA requirements

Within 6 Months

• Complete first proficiency testing cycle


• Conduct internal quality assessment


• Prepare for biennial survey

Ongoing

• Maintain quality control documentation


• Participate in proficiency testing (3x/year)


• Update personnel files and training


• Prepare for biennial surveys


• Renew certificate every 2 years

Related Regulations and Guidance

Federal:

• 42 CFR Part 493 (CLIA regulations)


• FDA regulations for in vitro diagnostic devices (21 CFR 809, 864)


• Clinical Laboratory Standards Institute (CLSI) guidelines

State:

• Massachusetts 105 CMR 170.000 (Laboratory Licensure)


• Massachusetts 244 CMR 2.00 (Blood Banks)

Quality Standards:

• ISO 15189 (Medical Laboratories - Quality and Competence)


• CAP accreditation standards


• COLA accreditation standards

Official Resources

• CMS CLIA Website


• 42 CFR Part 493 (eCFR)


• CMS Forms


• FDA CLIA Resources


• CDC CLIA Resources


• Massachusetts CLIA