CLIA has five certificates: Waiver for waived tests only, PPM for nine microscopy procedures plus waived tests, a temporary Registration certificate for new nonwaived labs, and Compliance or Accreditation for moderate and high complexity testing. Choose by the most complex test you run. Each is valid for two years.
Every CLIA lab holds one of five certificates. Which one depends on a single question: what is the most complex test the site performs? The CMS-116 instructions say to "select your certificate type based on the highest level of test complexity performed by your laboratory." CMS's application page adds two points that hold for every type: all certificates are effective for two years, and all of them allow waived testing.
The September 2026 CMS statistics show how lopsided the field is. Of 285,940 labs registered outside New York and Washington, 233,448 hold a Certificate of Waiver, 21,736 a PPM certificate, 15,214 a Certificate of Compliance and 15,542 a Certificate of Accreditation.
How is test complexity decided?
FDA categorizes each test system as waived, moderate complexity or high complexity, and its CLIA database is where you check. Provider-performed microscopy is a subcategory of moderate complexity (42 CFR 493.19(b)(2)). Two default rules matter. CMS's home testing FAQ says "any test that has not been categorized is considered high complexity by default," and that a waived kit used off-label "defaults to high complexity." Our post on how to tell whether a test is CLIA-waived covers the lookup.
Which certificate fits a site that runs only waived tests?
The Certificate of Waiver. It is "issued to a laboratory that only performs waived tests" (Quick Start Guide, March 2026). The lab must follow each manufacturer's instructions (493.15(e)), name a director, and notify the State Agency before testing anything beyond waived (493.39). Federal rules set no qualifications for its director. Waiver labs are "not routinely surveyed," though they can be inspected on a complaint or to check that they are staying within the certificate (493.1775). The CMS fee as of October 2026 is $248 for two years. Start with the Certificate of Waiver, start to finish.
When is a PPM certificate the right choice?
The Certificate for Provider-Performed Microscopy Procedures covers nine microscopy procedures, such as wet mounts, KOH preparations and urine sediment exams, plus waived tests. The procedures must be "personally performed" by a qualifying practitioner "during the patient's visit" with a brightfield or phase-contrast microscope (493.19). The director must be a physician, a midlevel practitioner authorized by the state to practice independently, or one of the other practitioners the rule names, and may direct no more than five labs (493.1357, 493.1359). PPM labs are not routinely surveyed (493.47(c)(3)). The CMS fee as of October 2026 is $297. Details in the PPM certificate and the nine microscopy procedures.
Why do nonwaived labs start with a Certificate of Registration?
A lab adding moderate or high complexity testing cannot go straight to a Compliance or Accreditation certificate. It first receives a Certificate of Registration, which the Quick Start Guide describes as issued "to temporarily allow the laboratory to conduct nonwaived (moderate and/or high complexity) tests until the laboratory is inspected and found to be in compliance." Only labs applying for Compliance or Accreditation receive one, it is valid for no more than two years (493.45(e), 493.57(d)), and the registration fee is $123 as of October 2026. A lab holding a Certificate of Waiver that wants to add nonwaived tests needs one too (493.45(a)(2)). See the Certificate of Registration and the first survey.
Compliance or Accreditation: what separates the two nonwaived certificates?
Both allow waived, PPM, moderate and high complexity testing, and both require a director who meets the subpart M qualifications, proficiency testing, quality control and survey every two years. The difference is who inspects.
- Certificate of Compliance. Issued after "the State Agency or CMS surveyor finds the laboratory in compliance with all applicable CLIA requirements." The lab pays a certificate fee and a separate compliance survey fee, both scaled by volume and specialties.
- Certificate of Accreditation. Issued on the basis of accreditation by a CMS-approved accreditation organization. The current CMS-116 lists seven: The Joint Commission, ACHC, AABB, A2LA, CAP, COLA and ASHI. The lab pays CMS a certificate fee and a validation fee, plus whatever the accreditation organization charges.
The Quick Start Guide frames it as a choice "based on the agency you wish to survey your laboratory." We compare them in Certificate of Compliance or Certificate of Accreditation? and list the organizations in the CLIA accreditation organizations.
How do the five compare side by side?
- Waiver. Waived tests only. No federal director qualifications. Not routinely surveyed. CMS fee $248.
- PPM. The nine PPM procedures plus waived tests. Director under 493.1357. Not routinely surveyed. CMS fee $297.
- Registration. Temporary; nonwaived and waived testing until the survey or proof of accreditation. Director under subpart M. CMS fee $123.
- Compliance. All complexities. Director under subpart M. State Agency survey every two years. CMS certificate fee from $223 to $11,801 by schedule, plus a survey fee.
- Accreditation. All complexities. Director under subpart M. Accreditation organization inspection every two years, with CMS validation surveys. CMS certificate fee from $223 to $11,801 by schedule, plus a validation fee.
All figures are CMS fees as of October 2026, from the fee schedule CMS links on its application page. The lab pays them to CMS on pay.gov from its own emailed coupon. See CLIA fees in 2026.
Where do most labs land?
CMS's September 2026 figures by facility type answer that from another angle. Of all 301,284 registered labs, including the exempt states, physician offices are the largest group at 116,814, about 39 percent. Pharmacies follow at 22,728, then skilled nursing facilities at 14,738, home health agencies at 13,021 and assisted living facilities at 11,095. Hospitals account for 9,257 and independent labs for 7,824. Most physician office labs hold a Certificate of Waiver (84,829 of the 114,313 outside New York and Washington), and 16,123 hold PPM certificates. If your site looks like a typical clinic, pharmacy or care facility, the decision is usually between a waiver and, for practices doing their own microscopy, PPM.
Can a lab change certificate types later?
Yes, with a new CMS-116 marked "Change in Certificate Type" and an effective date. Going up is the common move, and the order matters: a waiver lab "must notify HHS or its designee… before performing and reporting results for any test" outside its certificate (493.39(a)). CMS's waiver brochure is blunter: "you cannot begin nonwaived testing until you have paid the appropriate fee, and have received the appropriate certificate." Moving from PPM to nonwaived works the same way (493.53(a)). Going down, for example when a clinic drops its last moderate complexity test, is also a certificate-type change. More in moving from a waiver to moderate complexity testing.
Do state rules change the choice?
Not the federal choice, but they can add a second filing. CMS's application page notes that "some states may have additional licensing requirements," and labs there "must meet both the CLIA and state requirements." New York and Washington run their own programs, so most labs there follow state rules instead of filing the CMS-116. Check your state in the CLIA state requirements index and read state lab licensing on top of CLIA.
Which filings does White Glove CLIA handle?
Waiver and PPM certificates are our core work: $399 per site for a Certificate of Waiver Application and $599 per site for a PPM Certificate Application. For a lab moving into nonwaived testing, the Nonwaived Certificate Application Packet ($1,499) prepares the CMS-116 and the director qualification documents for the Registration and Compliance or Accreditation path. We do not act as or supply a laboratory director, build nonwaived quality systems or handle proficiency testing samples. Not sure which certificate fits? The CLIA Readiness Review is $149 and is credited toward a filing.
Common questions
- Which CLIA certificate do I need for rapid strep, flu and urine pregnancy tests?
- A Certificate of Waiver, as long as every test you run is FDA-categorized as waived and used exactly as its instructions say. If you add any microscopy or moderate complexity test, you need a different certificate first.
- What is the difference between a Certificate of Compliance and a Certificate of Accreditation?
- Both cover nonwaived testing. A Compliance lab is surveyed by the State Agency or CMS. An Accreditation lab is inspected by a CMS-approved accreditation organization such as CAP, COLA or The Joint Commission, and is subject to CMS validation surveys.
- Can a lab with a PPM certificate run waived tests?
- Yes. A PPM certificate covers the PPM procedures and waived tests. CMS says all certificate types allow waived testing.
- How long is a CLIA certificate valid?
- Each type is valid for no more than two years. A Registration certificate lasts no more than two years or until the lab's compliance is determined, whichever comes first.
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