Clinical Lab Setup Checklist: From CLIA Certificate to Go-Live
This is a master checklist for setting up a clinical laboratory in the United States, the kind that tests human specimens for diagnosis, treatment or health assessment and therefore falls under the Clinical Laboratory Improvement Amendments (CLIA). It is not a home-lab or research-lab guide. Use it to plan a new lab, add a testing specialty, or bring a new analyzer online, then open the manufacturer-specific checklist for the instruments you are installing. Sound Lab Consultants (SLC) is a nationwide clinical laboratory consulting network that helps labs set up instruments from all major manufacturers. SLC is independent and not affiliated with or endorsed by any instrument manufacturer.
Phase 1: Define your test menu and business case
Start with the tests your clinicians or clients actually order. Volume, turnaround expectations and reimbursement drive every later decision, from instrument choice to staffing. List each analyte, its expected monthly volume and the specialty it belongs to (chemistry, hematology, immunology, microbiology, molecular and so on).
List each test and expected volume
Estimate reimbursement and send-out cost per test
Decide what stays in-house versus reference lab
Identify space, utility and IT constraints early
Phase 2: Determine test complexity
CLIA classifies each test system as waived, moderate complexity or high complexity. The FDA publishes these categorizations in its CLIA database, searchable by analyte, test system and manufacturer. Look up every test on your menu and save the record. The highest complexity on your menu determines the certificate type and the personnel you need. Modifying an FDA-cleared test or developing your own test makes it high complexity.
Phase 3: CLIA certificate and CMS-116
Apply with Form CMS-116 through your State Agency. Waived-only labs apply for a Certificate of Waiver; labs performing moderate or high complexity testing receive a Certificate of Registration first, followed by a Certificate of Compliance after a state survey or a Certificate of Accreditation through a CMS-approved accrediting organization. Provider-performed microscopy has its own certificate. Some states run their own laboratory licensure programs, and several states license laboratory personnel, so check your state's requirements alongside CLIA.
Choose certificate type
Name a qualified laboratory director
List specialties and annual volumes
Check state licensure and personnel licensing
Pay CLIA fees when billed
Phase 4: Space, utilities and safety design
Map specimen flow from receipt to disposal. Confirm electrical capacity and dedicated circuits, uninterruptible power, water quality for analyzers that require purified water, drain access, HVAC capacity for instrument heat load, and room temperature and humidity ranges in each manufacturer's site requirements. Molecular labs need physical separation of pre- and post-amplification areas.
Electrical, UPS and network drops
Water purification if required
Temperature and humidity monitoring
Biosafety cabinet and eyewash placement
Waste streams and sharps
Phase 5: Instrument selection and purchasing
Compare analyzers on test menu fit, throughput, footprint, reagent cost per reportable result, service coverage, LIS connectivity and FDA categorization of each assay. Request site requirement documents, sample package inserts and the manufacturer's performance claims, because you will need them for verification. Negotiate service, training and reagent pricing together.
Phase 6: Install, verify and validate
Under 42 CFR 493.1253, before reporting patient results on an unmodified FDA-cleared or approved moderate or high complexity test, the lab must verify accuracy, precision and reportable range and confirm that reference intervals fit its patient population. Modified tests and lab-developed tests require establishment of performance specifications including analytical sensitivity, analytical specificity and any other characteristic required for test performance. The laboratory director reviews and approves the study.
Accuracy (method comparison)
Precision (within-run and day-to-day)
Reportable range
Reference interval verification
Director sign-off before patient testing
Phase 7: Calibration, QC and IQCP
Follow each manufacturer's calibration procedure and perform calibration verification at least every six months and when required by events such as major maintenance. Define your QC plan: CLIA's default is two levels of control per day of testing for most non-waived tests, or an Individualized Quality Control Plan built on a documented risk assessment. Set QC rules, review frequency and corrective action documentation.
Phase 8: Proficiency testing
Enroll in CMS-approved proficiency testing for every regulated analyte. Treat PT samples like patient samples, never discuss results with other labs before the deadline, and never send PT samples to another lab. For tests without required PT, perform an alternative assessment such as split-sample comparison at least twice per year.
Phase 9: Personnel under Subpart M
Moderate complexity labs need a laboratory director, technical consultant, clinical consultant and testing personnel. High complexity labs need a laboratory director, technical supervisor, clinical consultant, general supervisor and testing personnel. Qualifications depend on degree, training and experience. Keep primary source documentation, training records and competency assessments using the six CLIA elements.
Phase 10: SOPs, records and LIS
Write and approve a procedure manual covering every test, plus specimen collection and handling, test requisition, reporting, critical values, corrective action, complaint handling and record retention. Validate your LIS interface so results transmit accurately to the report. Build retention schedules that meet CLIA minimums and any longer accreditation or state requirements.
Phase 11: Accreditation
If you choose a Certificate of Accreditation, select a CMS-approved accrediting organization such as CAP, COLA or The Joint Commission. Download the applicable checklists or standards early and map them to your SOPs and records.
Phase 12: Go-live and ongoing compliance
Run a mock inspection before go-live, confirm all verification studies are signed, QC is in range, PT is enrolled and competency is documented. After go-live, schedule recurring tasks: calibration verification, competency, PT events, QC review, maintenance, and annual policy review.
Budgeting for a new clinical lab
Typical startup costs include instruments (purchase, lease or reagent rental), reagents and controls, PT enrollment, CLIA certificate and survey fees, accreditation fees if chosen, LIS and interfaces, renovation and utilities, safety equipment, and staff time for validation and training. Ongoing costs include reagents per reportable result, service contracts, PT, staffing and compliance work. Model both before committing to an instrument.
Choosing in-house versus reference lab testing
Bring a test in-house when volume, turnaround needs and reimbursement justify the instrument, reagent, QC, PT and personnel costs. Keep low-volume, esoteric or high-risk tests at a reference laboratory. Review the decision yearly as volume changes.
Common setup mistakes
Buying an instrument before confirming the complexity of each test
Starting patient testing before the CLIA certificate is active
Verification studies without director sign-off
No written QC plan or IQCP
PT not enrolled for every regulated analyte
Personnel files missing diplomas or competency records
SOPs copied from package inserts without lab-specific detail
Record retention basics
42 CFR 493.1105 requires keeping QC and patient test records at least 2 years, test procedures 2 years after discontinuation, PT records 2 years, test reports at least 2 years after reporting, and performance specification records for as long as the test system is in use but no less than 2 years. State or accreditation rules may require longer.
LIS and connectivity
Most analyzers connect to a laboratory information system through an interface or middleware. Validate each interface before go-live by sending results across the reportable range, including flags, comments and critical values, and confirming they appear correctly on the final report. Keep the validation records, and repeat checks after software upgrades or interface changes.
Working with your instrument vendor
Manufacturers typically provide installation, operator training and applications support for their own systems. Use that support, and keep copies of installation reports, training certificates and service records. The lab remains responsible for CLIA verification, QC, PT and personnel requirements regardless of vendor involvement.
Software: compliance tracking with myLabCompliance
Paper binders and spreadsheets break down once a lab has several instruments, shifts and testing personnel. For the document and people side of compliance, we recommend myLabCompliance, a web-based CLIA compliance management platform for technical consultants, lab directors, lab owners and quality teams.
Document control for SOPs, policies and procedure manual approvals
Training records for testing personnel
Competency assessment tracking for the six required elements
Proficiency testing scheduling and PT records
Keep instrument-generated QC, calibration and maintenance data in the systems your lab and manufacturer documentation specify.
Manufacturer-specific lab setup checklists
Each checklist below applies this framework to a specific manufacturer's instruments. Pages are being added in priority order.
Bio-Rad (checklist coming soon)
QuidelOrtho (Ortho Clinical Diagnostics) (checklist coming soon)
bioMérieux (checklist coming soon)
BD (Becton Dickinson) (checklist coming soon)
Hologic (checklist coming soon)
Thermo Fisher Scientific (checklist coming soon)
Werfen (Instrumentation Laboratory) (checklist coming soon)
DiaSorin (checklist coming soon)
Mindray (checklist coming soon)
Stago (checklist coming soon)
HORIBA Medical (checklist coming soon)
Nova Biomedical (checklist coming soon)
Radiometer (checklist coming soon)
QIAGEN (checklist coming soon)
Sekisui Diagnostics (checklist coming soon)
Illumina (checklist coming soon)
Tosoh Bioscience (checklist coming soon)
Snibe (checklist coming soon)
The Binding Site (Thermo Fisher) (checklist coming soon)
Grifols (Diagnostic) (checklist coming soon)
Supplies and consumables
SLC works with suppliers including Fisher Scientific/Thermo Fisher, Promega, QIAGEN, VWR/Avantor, Sartorius, Henry Schein, McKesson and Medline to help labs source consumables and general lab equipment.
Frequently asked questions
What is a clinical lab setup checklist?
A step-by-step plan covering test menu, CLIA certificate, space, instruments, verification, QC, proficiency testing, personnel, SOPs and accreditation for a lab that tests human specimens.
How do I know what CLIA certificate I need?
Look up each test in the FDA CLIA database. Waived-only labs need a Certificate of Waiver; moderate or high complexity testing requires a Certificate of Compliance or Accreditation.
Which form starts a CLIA application?
Form CMS-116, submitted through your State Agency.
Do I have to verify a new FDA-cleared analyzer?
Yes. 42 CFR 493.1253 requires verification of accuracy, precision, reportable range and reference intervals before reporting patient results.
Does SLC work nationwide?
Yes. SLC is a nationwide clinical laboratory consulting network. Plans from $500.
Sound Lab Consultants (SLC), PO Box 2135, Chandler, AZ 85244. A nationwide clinical laboratory consulting network. Plans from $500.
More SLC services: CLIA consultant, laboratory director services, laboratory consulting company, CAP laboratory consultant, COLA laboratory consultant.