How Many Sites for a CLIA Waiver Study? Three Minimum, Nine Untrained Operators

FDA recommends that a study supporting CLIA waiver be run at a minimum of three sites that represent both the intended-use patient population and the intended operators in CLIA-waived settings, with 1–3 untrained operators at each site and at least nine untrained operators across all sites. Those operators should be staff already employed at the sites, with no prior training on the candidate test, working from only the instructions that will ship with the product. Three sites and nine operators are floors, not targets: enrollment, prevalence and reproducibility design usually push a real study above them.

The numbers come from FDA’s guidance Recommendations for Clinical Laboratory Improvement Amendments of 1988 (CLIA) Waiver Applications for Manufacturers of In Vitro Diagnostic Devices (issued February 26, 2020; referred to below as the CLIA waiver guidance). Its companion, Recommendations for Dual 510(k) and CLIA Waiver by Application Studies (also February 26, 2020; the dual guidance), adds per-operator sample minimums and reproducibility-site rules. Both are nonbinding guidance, so a sponsor can propose an alternative, but the expected route for that is a Pre-Submission. Everything quoted below is from those two documents or from the CLIA regulations at 42 CFR Part 493.

What does the FDA guidance actually require for sites and operators?

The site and operator recommendations sit in Section V.C of the CLIA waiver guidance. The core text, verbatim:

“You should conduct the study to support CLIA waiver at a minimum of three sites that are representative of both the intended use patient population and the intended operators in CLIA-waived settings. Generally, the sites should include different demographic and geographic locations (e.g., outpatient clinic, physician’s office), since patient populations and intended operators typically vary among different demographic locations.”

“The study should include 1-3 untrained operators at each site and at least nine (9) untrained operators across all sites.”

Taken together with the surrounding text, the requirements break down as follows.

Element	What the CLIA waiver guidance says
Number of sites	”a minimum of three sites”
Site character	Representative of the intended-use patient population and intended operators in CLIA-waived settings; generally different demographic and geographic locations
Untrained operators per site	”1-3 untrained operators at each site”
Untrained operators overall	”at least nine (9) untrained operators across all sites”
Who the operators are	”personnel currently employed in the selected intended use sites”
Workflow	Testing “integrated into the daily workflow of the facility where the operators are often multitasking between patient care, testing, and other duties”
Site reporting	Name, address and study dates for each site; a brief explanation for any site that started but did not complete
Specimens	Prospective specimens preferred, from “consecutive patients over one month” (two weeks may be appropriate depending on site and prevalence)
Archived or surrogate samples	”In general” no more than one third of total study samples, with justification

Note the arithmetic built into the two operator rules. If each site may hold at most three untrained operators and you need at least nine, then three sites only works if every site supplies three operators. Lose one operator at one site and you are at eight, below the floor. That is one practical reason studies are commonly planned with more than three sites.

Why is three sites a floor and not the plan?

Three sites meet the letter of the guidance; they rarely meet the study’s other constraints. The guidance asks for specimens that “adequately represent all possible values of the test,” including samples near the cutoff for qualitative tests and around medical decision levels for quantitative ones, and it prefers prospective, consecutive enrollment. For a seasonal or low-prevalence analyte, three sites may not produce enough positives inside a reasonable window.

The operator ceiling compounds this. Because each site is capped at three untrained operators, the only way to add operators (and the specimens they test) is to add sites. The table below shows how the site count and the operator floor interact, using the dual guidance’s per-operator minimum of five comparator-positive and five comparator-negative samples for binary qualitative tests.

Sites	Max untrained operators (3/site)	Meets ≥9 operators?	Minimum positives at 5 per operator (if exactly 9 operators)
3	9	Only if every site enrolls 3	45
4	12	Yes, with slack	45
5	15	Yes, with slack	45

The 45-positive figure is a mathematical floor derived from two guidance recommendations, not a sample size FDA endorses. Your actual sample size is driven by the precision you need on sensitivity or positive percent agreement. Using a two-sided 95% Wilson score interval (FDA’s 2007 Statistical Guidance on Reporting Results from Studies Evaluating Diagnostic Tests points to score intervals for sensitivity and specificity):

Positives tested	Agreed	Point estimate	95% Wilson interval
45	45	100.0%	92.1% – 100.0%
45	44	97.8%	88.4% – 99.6%
45	43	95.6%	85.2% – 98.8%
60	58	96.7%	88.6% – 99.1%
100	98	98.0%	93.0% – 99.4%
120	117	97.5%	92.9% – 99.1%

Computed with z = 1.95996: lower bound = (p̂ + z²/(2n) − z·√(p̂(1−p̂)/n + z²/(4n²))) / (1 + z²/n).

At 45 positives, a single discordant result drops the lower bound below 89%. If your acceptance criterion is expressed as a lower confidence bound, that is the number that matters, and it typically requires more positives than the operator floor alone produces. More positives at a fixed prevalence means more enrolled subjects, and more enrolled subjects inside a one-month window usually means more sites.

What makes a site “CLIA-waived” and representative?

A CLIA-waived site, for these purposes, is a testing location operating under a CLIA Certificate of Waiver. Under 42 CFR 493.15(e), laboratories eligible for a certificate of waiver must “follow manufacturers’ instructions for performing the test” and meet the requirements of Subpart B (Certificate of Waiver). The personnel qualification standards in Subpart M are titled “Personnel for Nonwaived Testing”; CLIA itself sets no testing-personnel qualifications for waived testing. That is exactly why waived settings are staffed by people with a wide range of backgrounds, and why FDA wants to see the test perform in their hands.

The guidance gives “outpatient clinic, physician’s office” as examples. In practice, the settings where waived tests are run include urgent care centers, physician office laboratories, primary care and pediatric practices, retail and public health clinics, and specialty clinics relevant to the analyte. Holding a Certificate of Waiver is necessary but not sufficient. A site is representative when:

The patients match the intended use. A pharyngitis test belongs in sites that see sore throats; a sexual health assay belongs in sites that see those patients. The guidance asks for sites representative of “the intended use patient population.”
The staff match the intended operators. If the test is meant for medical assistants in a busy office, a site where all testing is done by a dedicated medical technologist is not representative, even if it holds a waiver certificate.
The workflow is real. The guidance is explicit that testing should be “integrated into the daily workflow of the facility.” A quiet back room where one person runs the study and nothing else does not replicate waived use.
The sites differ from each other. “Different demographic and geographic locations” is a design requirement, not a nice-to-have.

A dual submission for a point-of-care STI test illustrates the breadth this can require: its sites spanned OB/GYN offices, sexual health and STD clinics, primary care, public health, a student health clinic and an HIV clinic, because each is a place the test would actually be used.

Who counts as an untrained operator?

The CLIA waiver guidance defines an untrained operator, or waived user, as “a test operator in waived settings and with limited or no training or hands-on experience in conducting laboratory testing.” Section V.C(2)(a) adds that they “should not have previous training or experience with the candidate test, but may have limited experience with other waived or home use tests,” and that they “should be personnel currently employed in the selected intended use sites.”

FDA also states a preference that pushes enrollment toward the least experienced end of the plausible range: “We encourage you to enroll operators with the least amount of training that might be encountered at the types of sites for which this device is intended.”

Usually fits	Usually does not fit
Medical assistants, front-desk or clinical support staff who run waived tests among other duties	Medical technologists or clinical laboratory scientists
Nurses and other clinical staff without laboratory training, where they are the intended users	Anyone who has run the candidate test before, including in a feasibility or earlier study
Staff with limited experience of other waived tests (e.g., a urine pregnancy test)	Sponsor employees or contractors brought into the site
	Staff hired for the study rather than already employed at the site

The trained-operator side is defined by regulation. A trained operator, or moderate complexity laboratory user, is “a test operator who meets the qualifications to perform moderate complexity testing,” which points to 42 CFR 493.1423. For Option 4 and dual studies, trained operators run the comparative method “at an appropriate laboratory site” and should be qualified for and experienced with that method.

What training are untrained operators allowed to receive?

None beyond the product labeling. Section V.C(2)(c) is unusually direct:

“You should provide the untrained operators who participate in the study with only the instructions and training materials that are intended for untrained operators and are ‘simple’ … and that will be provided with the test kit in the actual intended use settings when the test is marketed. … The untrained operators should receive no additional instructions (e.g., written or verbal training, coaching, or prompting).”

The guidance adds that operators “should have no opportunity to discuss the test with other participants or otherwise coach or observe each other,” and that they “may call a toll-free help-line if such a service is to be provided for the device when it is marketed.” The instructions given to operators go into the waiver application, and labeling for a “simple” test should be written “at a 7th grade reading level, or lower.”

What this means operationally for a site initiation visit:

Train site staff on the protocol: consent, eligibility, specimen collection, labeling, case report forms, specimen shipping for the comparator, and adverse-event and deviation reporting.
Do not demonstrate the device, run a practice test in front of operators, or answer questions about the test procedure beyond what the labeling and any planned help line would answer.
Keep untrained operators from watching each other test. In small offices this needs explicit scheduling.
Record any contact with operators about the device. A monitor who “just helps” with a stuck step has created a deviation that FDA may view as coaching.

How does the dual 510(k)/CLIA waiver guidance change this?

In a dual submission, one set of comparison and reproducibility studies run by untrained operators supports both substantial equivalence and waiver. The dual guidance points back to the CLIA waiver guidance for sites and operators, and recommends Option 4: “comparison studies in which the results of the candidate test in the hands of untrained operators are directly compared to the results of an appropriate comparative method in the hands of trained operators.” So the three-site, nine-operator framework carries over. What the dual guidance adds:

Topic	Dual guidance recommendation
Comparison study, binary qualitative	”Each untrained operator should run the candidate test with a minimum of 5 samples that are positive by the CM and 5 samples that are negative by the CM.”
Reproducibility sites	”a minimum of 3 of the same sites that were included in the comparison study” and representative of waived use
Reproducibility operators	”the same number of untrained operators (likely 2 or 3) should be included at each site”
Sources of variability	Different sites, untrained operators, days, runs, lots (if applicable) and a few replicates
Lot-to-lot	Either three lots at each of three sites, or a separate small study at one internal site; one lot per site is “generally undesirable”
Non-waived POC sites	If the test is also intended for non-waived point-of-care sites whose patients are not represented, include “one or a few POC non-waived sites” with trained operators
Analytical studies	Conducted at an internal site (LoD, interference, cross-reactivity, stability and so on)

Two consequences are easy to miss. First, the reproducibility sites must be drawn from the comparison-study sites, so a site you plan to use for reproducibility has to be selected, qualified and kept engaged from the start. Second, the per-operator sample minimum makes uneven enrollment a real risk: an operator who works two days a week at a low-prevalence site may never reach five comparator-positive samples. Sites, schedules and operator selection therefore need to be planned together.

The CLIA waiver studies and dual submission studies pages describe how these two routes differ in sequencing. In short, a sequential waiver application follows clearance and, in FDA’s view, will usually fit Option 1 (untrained versus trained operators on the same cleared test), while a dual study builds the untrained-operator evidence into the 510(k) itself.

What does a real site and operator plan look like?

Published decision summaries give a sense of the range. Three case studies from dual submissions:

A point-of-care fingerstick PT/INR system used four sites holding CLIA waiver certificates and 11 untrained operators for method comparison, with reproducibility at three external waived sites with two untrained operators per site.
A point-of-care molecular Strep A test ran its prospective study at nine point-of-care sites, with testing by non-laboratory health professionals representative of intended users, and a near-cutoff reproducibility study at three waived sites with two operators each.
A rapid antigen influenza A/B test needed 21 point-of-care sites in a single season, plus masked banked specimens worked into the daily workflow at three of them, because influenza B prevalence was atypically low that year.

None of these stopped at three sites. In each case the binding constraint was specimens, not the operator floor.

How should site and operator selection be documented?

The guidance expects documentation of both who was chosen and who was not:

“We recommend that you record and tabulate the education (including experience and training) and the occupation of each untrained operator to demonstrate that these participants meet the definition of intended operators and include this in your CLIA waiver application. In addition, for each study site, we recommend you report the same information on other personnel that were available at the testing site but that were not chosen to participate.”

The second sentence is the one that catches sponsors. FDA is looking for selection bias: a site with five eligible staff where the two most technically experienced were chosen is a different study from one that picked at random or picked the least experienced. A practical documentation set:

A site profile per site: setting type, CLIA certificate type, patient volume for the intended population, and a brief description of how waived testing fits the daily workflow.
An operator roster per site listing every person who could plausibly run the test, with education, occupation, laboratory training and experience, and whether they were enrolled.
A signed operator attestation of no prior exposure to the candidate test.
The exact labeling version given to operators, and a log of any help-line or monitor contact.
The post-study operator questionnaire, administered “after the completion of the clinical study, so the questions do not bias the untrained operators.”

For each untrained and trained operator, the clinical study report should also give total tests performed, initial invalids, retests and final invalids, with the invalid rate reported with a two-sided 95% confidence interval.

What are the common ways site and operator plans fail?

Planning exactly three sites with three operators each. One resignation or one exhausted operator puts the study below nine.
Operators who are really laboratorians. A site whose testing is done by a laboratory-trained employee may hold a waiver certificate and still fail the “intended operators” test.
Contaminated naivety. Operators who joined a feasibility run, saw a sponsor demo, or watched a colleague test are no longer untrained for this device.
Non-representative workflow. A dedicated study coordinator running every test in isolation does not reflect “multitasking between patient care, testing, and other duties.”
Reproducibility sites chosen late. If they were not comparison sites, the dual guidance’s design is not met.
Uneven enrollment across operators. Some operators never reach five positives; others carry most of the data, which weakens any claim about operator-to-operator robustness.
No record of who was not chosen. Easy to collect at start-up, very hard to reconstruct afterward.

A Pre-Submission is the place to settle site count, operator mix and comparator choice before enrollment; both guidances encourage it.

How Studybox approaches this

Studybox Research works only on IVD studies, and its team has supported 55+ FDA regulatory clearances across 510(k), dual 510(k)/CLIA waiver, OTC and EUA pathways. The network includes 100+ pre-qualified U.S. urgent care, physician office and point-of-care sites, which makes it practical to plan above the three-site floor and to choose sites by patient population and staffing rather than by availability. What “pre-qualified” should mean covers how that readiness is assessed.

Typical activation is about four weeks, against a 3–6 month industry average, which matters when a waiver study has to land inside a respiratory season. If you are sizing a waiver or dual study, contact us with your intended use and target performance and we can work through site and operator numbers with you.

Studybox Research Guide October 5, 2026