One CLIA Certificate per Site, and the Three Exceptions

A CLIA certificate belongs to a place. The federal rule for a Certificate of Waiver says a laboratory performing only waived tests "must file a separate application for each laboratory location," except in the cases the rule lists (42 CFR 493.35(a)). The rules for PPM, registration, compliance and accreditation certificates say the same thing in nearly the same words (493.43(a) and 493.55(a)(2)). So the default answer for a practice group, an urgent care group or a pharmacy chain is simple: every fixed location that tests gets its own CMS-116, its own CLIA number and its own fee.

There are exactly three exceptions. They are narrower than most people expect, and CMS tells State Agencies to apply them with care. The State Operations Manual says "Caution should be used when determining if an entity can be issued one certificate for multiple sites" and that "Each exception stands alone and must not be combined with another exception" (SOM Chapter 6, section 6010, Rev. 230, July 2025).

What are the three exceptions?

All three appear in 42 CFR 493.35(b), and again in 493.43(b) and 493.55(b) for the other certificate types. Section V of the CMS-116 asks about each one by number.

1. Labs that are not at a fixed location. "Laboratories that move from testing site to testing site, such as mobile units providing laboratory testing, health screening fairs, or other temporary testing locations may be covered under the certificate of the designated primary site or home base, using its address."
2. Limited public health testing. "Not-for-profit or Federal, State, or local government laboratories that engage in limited (not more than a combination of 15 moderately complex or waived tests per certificate) public health testing may file a single application."
3. Hospital labs on one campus. "Laboratories within a hospital that are located at contiguous buildings on the same campus and under common direction may file a single application or multiple applications for the laboratory sites within the same physical location or street address."

The CMS-116 instructions add one more line under Section V: "Hospice and HHA could qualify for an exception." That is not a fourth exception. It points home health agencies and hospices to the first one, because their staff test in patients' homes, which are temporary testing locations.

How does the mobile and temporary site exception work?

The site that holds the certificate is the home base, and the certificate uses its address. On the CMS-116, "a list of temporary testing sites must be included on or attached to the Form CMS-116," and if a mobile unit does the testing, you "record the vehicle identification number(s) (VINs) and attach to the application."

CMS defines a mobile unit as "a movable, self-contained operational laboratory with its own personnel, equipment, and records, with equipment installed and located permanently within the mobile unit." A car that carries a waived analyzer from the clinic to an event is not one: "If a vehicle is used solely to transport laboratory equipment from the primary site/home base to another site where testing is performed, the transporting vehicle is not a mobile unit" (SOM section 6010.1). The State Agency also expects a phone number at the home base or central dispatch so it can get the current schedule of testing locations and hours.

When the list of temporary sites changes, the lab sends written notice, and for testing in patients' homes, "no individual addresses need to be submitted but should be available upon request" (SOM section 6016.1). Our post on mobile units and temporary testing sites goes further.

Who qualifies for the public health exception?

This exception is the one chains most often hope to use, and the one they almost never fit. CMS spells out the limits in SOM section 6010.2:

• The facility must be not-for-profit or a federal, state or local government facility; CMS gives WIC clinics as an example and notes that "Not-for-profit status is a legal designation."
• The testing is limited to 15 or fewer tests, and those tests must be listed on the application. A Certificate of Waiver lab "is eligible if it only performs 15 or fewer waived tests."
• Every site under the certificate may perform only the tests listed. Any high complexity testing disqualifies the entity.
• The primary site named on the application "must perform testing and hold the certificate," and it must identify the testing performed at each site.

CMS also says "Limited public health testing is not defined in the regulation." That leaves the State Agency room to decide whether a given program qualifies. A county health department running the same short menu at several clinics is the textbook case. A for-profit company is outside it by definition, however short its menu.

Which labs count as hospital labs for the campus exception?

Only hospitals, including teaching hospitals of universities. "Other types of entities are not eligible." Common direction means every site is under the same laboratory director. The street address is the physical location of the main laboratory as assigned by the post office (SOM section 6010.3).

CMS adds a warning that matters to health systems: "The fact that the laboratory is owned by a hospital does not necessarily make it a hospital laboratory for purposes of the multi-site exception. In many of these cases, a multiple site certificate CANNOT be issued." A hospital-owned primary care practice across town is a separate location with its own certificate.

Why can't a for-profit chain file once?

Because none of the three exceptions describes it. A chain of urgent care clinics, retail pharmacies or med spas tests at fixed addresses (so the first exception does not apply), is not a not-for-profit or government lab (so the second does not apply), and is not a hospital (so the third does not apply). Each clinic or store files its own CMS-116, receives its own 10-character CLIA number and pays its own certificate fee. The current CMS fee for a Certificate of Waiver, as of October 2026, is $248 per site every two years.

The separate certificates are not just paperwork. Each one carries its own director name, test menu, expiration date and change obligations, and Medicare edits lab claims at the certificate level. A test billed under the wrong location's number, or from a site whose certificate lapsed, is a claim problem as well as a compliance problem. See putting the CLIA number on claims.

Can two labs share one address?

Yes, in the other direction. CMS allows "Multiple laboratories" to "operate at the same physical location... with separate CLIA numbers, as long as each laboratory can demonstrate that it is operating as a separate and distinct entity." If they share testing staff and equipment, their records must be kept separate, and "The times of testing cannot overlap and cannot be simultaneous" (SOM section 6009). CMS also asks that they not be called "shared laboratories."

Do state licenses follow the same rule?

Mostly, with differences that matter for multi-site operators. California's registration and license law copies the three federal exceptions and adds a fourth: "Locations within a single street and city address that are under common ownership may apply for and obtain a single license or registration or multiple licenses or registrations, at the discretion of the owner or owners" (Cal. Bus. & Prof. Code 1265(d)(4)). New York's Limited Service Laboratory program allows a multi-site registration only for government-owned labs or "sites operated under the same not-for profit corporation," and every site may run only the tests on the primary site's certificate. Check each state on the state requirements index before you plan a rollout.

How do we handle a multi-site rollout?

We start by checking whether any exception truly applies; usually none does. Then we build one CMS-116 per location from a shared test menu, adjust each for its own director, hours and volume, and add any state registration the location needs. The owner or director of each lab reviews and signs its application, and the signed forms go to the State Agency. CMS emails each fee coupon to the lab's own address, and the lab pays on pay.gov; we never collect or forward the CMS fee.

Our Multi-Site Waiver Package covers five sites for $1,599, and groups of 10 or more sites are $249 per site. Renewal and Compliance Tracking is $299 per year for the first lab and $99 per year for each additional site, which keeps every expiration date, 30-day change notice and emailed coupon on one calendar. For the basics of the certificate itself, start with the Certificate of Waiver, start to finish or the Certificate of Waiver hub.