Last updated: November 2026
A CLIA laboratory start-up is the work of choosing the right federal certificate under the Clinical Laboratory Improvement Amendments (CLIA), applying through the State Agency, and writing the quality system, procedures and records that 42 CFR Part 493 requires for nonwaived tests. Integral Healthcare Solutions (IHS) drafts the documents; the laboratory director approves the technical content, and the owner signs and files the application. IHS is a consulting firm, not a law firm.
What does a new laboratory need under CLIA before it tests patients?
It needs a CLIA certificate that fits the most complex testing it will perform, or CLIA-exempt status, and for nonwaived tests it needs written quality system policies and verified test performance before it reports patient results. Sources opened November 4, 2026: 42 CFR Part 493 (eCFR text with amendments through October 8, 2026); and the CMS documents How to Obtain a CLIA Certificate (revised November 2026), Apply for a CLIA Certificate, the CLIA Certificate Fee Schedule (updated 2024) and the List of Exempt States (August 15, 2025).
Under 493.3(a), a laboratory is cited as out of compliance with section 353 of the Public Health Service Act unless it holds a current, unrevoked or unsuspended certificate that applies to its category of examinations, or is CLIA-exempt, subject to 493.3(b). CMS: “If a facility performs even one test on human samples to assess health or to diagnose, prevent, or treat any disease, it’s considered a laboratory under CLIA and must apply for and get a CLIA certificate.”
Section 493.3(b) excludes forensic-only testing, research laboratories that do not report patient-specific results for diagnosis, prevention or treatment of disease or for assessing individual patients’ health, and drug testing by a laboratory certified by the Substance Abuse and Mental Health Services Administration (SAMHSA) that meets SAMHSA guidelines.
Which certificate does a start-up take?
Apply for the certificate that matches the highest level of test complexity the laboratory performs. CMS says every certificate type is effective for two years and allows waived testing.
| Certificate | Issued to | Surveys |
|---|---|---|
| Waiver | Only waived tests. | No routine surveys; a complaint can bring an unannounced one. |
| Provider-performed microscopy (PPM) | Listed microscopy done by a physician, midlevel practitioner or dentist during a patient visit. | Same as waiver. |
| Registration | A laboratory applying for a compliance or accreditation certificate. | Allows nonwaived testing until the initial survey; valid no more than two years or until inspection, whichever is shorter (493.45(e)). |
| Compliance | Nonwaived testing, after a survey finds compliance. | Every two years. |
| Accreditation | Nonwaived testing, based on accreditation by a CMS-approved organization. | Every two years, by the accreditor. |
Does every location need its own application?
For nonwaived testing, yes: 493.43(a) requires a separate application for each laboratory location, except as 493.43(b) provides. Mobile and other site-to-site laboratories may be covered by the primary site’s certificate. Not-for-profit or government laboratories doing limited public health testing, no more than a combination of 15 moderately complex or waived tests per certificate, may file one application. Hospital laboratories at contiguous buildings on the same campus and under common direction may file one or several applications for the sites within the same physical location or street address.
Who signs, and what does the application describe?
Under 493.43(c), an owner, or an authorized representative who attests that the laboratory will be operated in accordance with the requirements the Secretary established under section 353 of the Public Health Service Act, signs. The application lists the test procedures and annual number of each (excluding waived tests and tests for quality control, quality assurance or proficiency testing), each methodology, and personnel qualifications.
CMS sequence: complete Form CMS-116, send it to the State Agency where the laboratory is located, pay the fee once notified, receive the certificate by email, then begin testing. A laboratory in a state with extra licensing requirements must meet both.
Who needs a CLIA start-up and what triggers it?
A practice, clinic, pharmacy or new laboratory that will test human specimens without the certificate that fits its test menu needs this work.
- A waiver or PPM laboratory adds nonwaived tests. It reapplies on Form CMS-116 and cannot use the new certificate until it has paid any additional fees and received it.
- A new site starts nonwaived testing and needs its own application unless an exception in 493.43(b) applies.
- Ownership that affects the tax ID, or the name, location or director, changes. CMS says to notify the State Agency within 30 days.
CMS says a laboratory in New York or Washington, which run their own HHS-approved programs, may not need a CLIA certificate. This page covers the federal path; IHS’s NYSDOH CLEP page covers New York’s program.
How IHS helps a CLIA start-up
IHS reviews the test menu, locations and staffing against Part 493, maps each requirement to a procedure and a record, and drafts what is missing. Thomas G. Goddard, JD, PhD, IHS founder and former URAC Chief Operating Officer and General Counsel, leads the work in IHS’s Compliance Services line, with compliance program development as the program-build companion.
What IHS drafts
- A procedure manual shell that follows the contents list in 493.1251(b), which has 14 items where they apply to the test.
- Quality system policies for the preanalytic, analytic and postanalytic phases and general laboratory systems (493.1200(a)), including quality assessment (493.1200(b)).
- Protocol templates for the performance verification or establishment 493.1253 requires before patient results are reported.
- Storage and operating criteria for reagents, specimens and test systems (493.1252(b)).
- A personnel competency policy (493.1235), staff file templates, and a proficiency testing plan and log (493.801).
- A test report and result-transmission procedure (493.1291), and a mock review of the records.
What you supply
You supply the test menu and methods, the director, the owner’s signature, the test systems you select, the verification data your staff generate, staff records and proficiency testing enrollment.
The real limit
IHS does not choose or verify test methods, run the verification studies, direct the laboratory or perform tests. Section 493.1251(d) says: “Procedures and changes in procedures must be approved, signed, and dated by the current laboratory director before use.” Under 493.1407 for moderate complexity and 493.1445 for high complexity, the director must be onsite at least once every 6 months, with at least 4 months between the minimum two visits, and may direct no more than five laboratories. On October 8, 2026 CMS published a proposed rule (CMS-3478-P, 91 FR 64480; comments requested by December 7, 2026) that would change several sections cited on this page, including the director onsite-visit text in 493.1407(c) and 493.1445(c). A proposed rule is not in force; this page states the rules in effect on the date shown.
What to have ready for a CLIA start-up
Gather these before the first session. Each ties to 42 CFR Part 493.
- Your test list, each test marked waived, moderate or high complexity (493.5(a)).
- The address of every testing location (493.43(a)).
- The director’s name, state license if the state requires one, and qualifications for your complexity level (493.1405 moderate, 493.1443 high).
- The owner or authorized representative who will sign Form CMS-116 (493.43(c)(2)).
- Methodology, expected annual volume and personnel qualification records for each nonwaived test (493.43(c)(3)).
- Your plan for verifying or establishing performance specifications (493.1253).
- Your proficiency testing program and enrollment status (493.801).
- Your report format and how results reach the ordering provider (493.1291).
The free introductory call is where IHS walks through this list with you.
How does the federal certificate route compare with accreditation?
A laboratory with nonwaived tests, other than a PPM-only laboratory, can take the compliance route or the accreditation route; a waived-only laboratory takes neither. IHS ranks none of them.
| Route | How it works | Fees CMS lists |
|---|---|---|
| Compliance | Registration certificate, then a State Agency or CMS survey, then the compliance certificate. | Registration, compliance survey and compliance certificate fees, plus revisit fees. |
| Accreditation | Accreditation by a CMS-approved organization (AABB, A2LA, ACHC, ASHI, COLA, CAP or The Joint Commission), plus a CMS certificate. | Registration, accreditation certificate and validation survey fees, plus the accreditor’s fees. |
The route changes who surveys the laboratory and which fees apply, not whether Part 493 applies. IHS’s page on ACHC clinical laboratory accreditation covers one accreditor’s program; CAP versus COLA compares two others.
What does a CLIA certificate cost?
CMS publishes certificate and survey fees that depend on certificate type and annual test volume, and the State Agency tells each laboratory what it owes. See the CMS CLIA Certificate Fee Schedule (page opened November 4, 2026; the schedule is marked updated 2024). Verify current fees with CMS or your State Agency.
The cost of an IHS start-up depends on whether the laboratory performs waived or nonwaived tests, how many locations it has, and how much of the procedure manual, quality plan and personnel records already exist.
IHS scopes each engagement after a free introductory call.
What this is not
- It is not legal advice. IHS is a consulting firm, not a law firm.
- It is not a guarantee that a certificate will issue or a survey will go well.
- IHS does not file with, contact or correspond with CMS or a State Agency. The owner signs and files the application.
- It does not cover state laboratory licensing, which is separate.
Frequently asked questions
Do I need a CLIA certificate to test a single patient sample?
Generally yes. CMS says a facility that performs even one test on human samples to assess health or to diagnose, prevent or treat disease is a CLIA laboratory and must get a certificate.
Can a new laboratory test patients while it waits for its survey?
A laboratory doing moderate or high complexity testing receives a registration certificate first, and CMS says that certificate allows nonwaived testing until the laboratory is surveyed. Under 493.1253(b), a laboratory that introduces an unmodified, FDA-cleared or approved test system must still show comparable accuracy, precision and reportable range, and verify reference intervals, before reporting patient results.
Which CLIA certificate does a start-up need?
The one that matches the most complex testing it performs: a waiver certificate for waived-only laboratories, or a compliance or accreditation certificate, after registration, for moderate or high complexity tests.
What must a nonwaived laboratory have in writing?
Section 493.1200(a) requires written policies and procedures that implement and monitor a quality system for all phases of testing, and 493.1251(a) requires a written procedure manual for all tests that personnel can reach and follow. IHS drafts both for the director to approve.
Is proficiency testing required?
Generally yes for nonwaived testing. Section 493.801, in the subpart for nonwaived testing, says each laboratory must enroll in an HHS-approved proficiency testing program that meets the criteria in subpart I, for each specialty and subspecialty for which it seeks certification. For tests that subpart I does not cover, the laboratory instead must establish and maintain the accuracy of its testing procedures under 493.1236(c)(1).
What does the laboratory director need to meet?
A moderate complexity laboratory needs a director who meets 493.1405, and a high complexity laboratory one who meets 493.1443. Both require a state director license where the state requires one. CMS says a waiver laboratory must have a director but sets no federal education or experience qualifications.
Which states run their own program?
CMS names New York and Washington. Its exempt-states list (August 15, 2025) gives the Washington Medical Test Site Program and the New York Clinical Laboratory Evaluation Program. The CMS brochure says New York has a partial exemption, so a laboratory there asks the state.
Does IHS file with CMS or the State Agency?
No. The owner or authorized representative signs the application and sends it to the State Agency. IHS does not contact or correspond with CMS or the State Agency.