CLIA certificate of waiver for drug testing: how to apply in Texas

The short answer

To run instant drug test cups in Texas, complete form CMS-116 (choosing Certificate of Waiver) and the Texas HHSC supplement, Form 3225, and send them to the Texas CLIA state agency; email is the preferred method. CMS then emails a fee coupon; pay the Certificate of Waiver fee, $248 for two years as of 2026, online through pay.gov. The certificate arrives by email, and you put its 10-character CLIA number on your claims and in each payer's file. Renew every two years by paying the next coupon on time, and follow the test maker's instructions every time you test.

Who needs a certificate of waiver

The federal Clinical Laboratory Improvement Amendments (CLIA) cover any site that tests human specimens to diagnose, prevent or treat a condition, or to assess health. A treatment program that reads a urine cup and uses the result in a client's care is doing exactly that, even if no one there calls it a lab. The rules are at 42 CFR Part 493.

Your situation	What you need
You read instant cups or dip cards on site (IOP, PHP, outpatient, prescriber office)	A Certificate of Waiver for that location
You only collect specimens and send them to a reference lab	Usually no certificate for you; the lab holds its own. Keep the lab's CLIA certificate on file.
You run tests that aren't waived (an on-site analyzer, for example)	A different certificate (such as compliance or accreditation) with personnel and inspection requirements; this guide doesn't cover those
A sober living home tests only to enforce house rules	Not settled everywhere; ask the state agency and keep the answer in writing (see sober living drug testing policy)

On our Texas SUD program roadmap, "Get a CLIA certificate of waiver for in-office tests" comes after the organization NPI and the lease, because the application asks for the site address and the business's details. If you won't test on site, skip it and send everything to a lab.

Check that your tests are waived

• Waived status belongs to the exact device, not to drug testing in general. Before buying cups, look up the brand and model in the FDA's CLIA database and confirm it's categorized as waived for the specimen you'll use (urine or oral fluid).
• Keep the package insert for each device and lot in your testing binder. It's your procedure, and surveyors compare what staff do with it.
• Changing brands? Check the new device's status first and update the test list you gave the state agency.

How to apply, step by step

1. Gather what the form asks for: the legal business name exactly as on the IRS letter, the EIN, the testing site's physical address, a mailing address, an email address that someone reads (CMS now sends everything by email), the director's name, the hours you'll test and the list of waived tests.
2. Complete CMS-116 and check "Certificate of Waiver." CMS's certification quick start guide walks through it.
3. Complete the Texas supplement, HHSC Form 3225, Application for Certification, Supplement to CMS-116. HHSC won't process it until the CLIA regional office has everything it asked for. The form directs questions to Health Facility Compliance ([email protected]); confirm the current submission address there.
4. Send both to the state agency, by email where possible; mail and fax are also accepted.
5. Pay the fee coupon when it arrives by email. CMS no longer mails certificates or paper fee coupons, and from March 1, 2026 labs must pay CLIA fees online through pay.gov; paper checks aren't accepted (CMS paperless FAQ).
6. Receive the certificate by email with your CLIA number. Post or file it where a surveyor can see it; we keep it in the survey binder next to the HHSC license.
7. Load the CLIA number into your EHR's billing settings and each payer's enrollment record before you bill a single test (next section).

Don't start testing before the certificate is in force. If you're opening a new program, file the CLIA application while the HHSC license application is pending, so both arrive before your first client. That's how we sequence it in the IOP / PHP Program Launch.

What it costs

Item	Cost	Notes
Certificate of Waiver fee	$248 every two years	After the 2024 CLIA fee rule (CMS-3326-F), state CLIA programs list $248 for a two-year Certificate of Waiver (example: Minnesota's CLIA fee page); fees are adjusted every two years
Texas Form 3225	Check HHSC	Submitted with the CMS-116
Test devices, controls, gloves, temperature strips	Your supplier's price	Our program budget model carries a monthly line for drug testing supplies and lab work

Filling in CMS-116

For a Certificate of Waiver, the form tells you to complete sections I to VI and IX to X; the other sections are for non-waived testing. The places programs most often get stuck:

Section	What to watch
General information	The facility name must match your other records exactly, and the address must be where tests are performed, not a billing office or PO box. Give an email that will still work in two years; that's where renewal coupons go.
Type of certificate	Certificate of Waiver. Don't pick a higher certificate "to be safe"; it brings surveys and personnel rules you don't need.
Type of laboratory	Pick the facility type that best describes your program from the form's list; the state agency can tell you which fits a licensed treatment facility.
Hours of testing	The hours your program actually collects and reads tests
Multiple sites	"No" unless you clearly fit an exception (see below)
Waived testing	List the tests and estimate the yearly volume. Estimate honestly from your census and testing policy.
Ownership, director and signature	The director is legally responsible for the testing. The form's education and experience requirements apply to directors of non-waived testing; for a waived site, name the person who will answer for the testing, often the medical director or clinical director. The signature must be original or as the agency accepts.

More than one location

Under 42 CFR 493.35, a site that runs only waived tests generally files a separate application for each location. The exceptions are narrow: sites without a fixed location (mobile units, temporary sites such as health fairs) can operate under a home base's certificate; not-for-profit or government labs doing limited public health testing can file one application for up to 15 waived or moderate-complexity tests; and hospital labs on one campus have their own rule. A treatment program with a second office across town should plan on a second certificate, and should time it with the second location's license (see relocating a treatment program if you're moving instead).

After approval: claims and payer files

• Put the CLIA number on the claim. On the CMS-1500 it goes in box 23; on an electronic 837P claim, in the claim's REF segment with qualifier X4. Your EHR or clearinghouse should add it automatically once it's in your settings.
• Medicare: add the QW modifier. CMS recognizes a waived test on a claim by the QW modifier, for example 80305-QW for a presumptive drug test read by direct optical observation, and pays only when the performing site holds a certificate that covers the test (CMS MLN MM13253). A short list of codes doesn't need QW; drug tests aren't on it.
• Texas Medicaid: the CLIA data must be in PEMS. HHSC told Medicaid managed care plans to edit lab claims against the CLIA information in each provider's PEMS enrollment: a soft edit through May 31, 2026, then hard denials for dates of service on and after June 1, 2026 when the CLIA certificate on file doesn't cover the billed procedure code (Community Health Choice notice of HHSC's timeline). Update your record through TMHP's PEMS licenses page.
• Commercial plans: send each plan the certificate with your credentialing packet, and check its medical policy on drug testing before you bill. Many limit how often and what they pay for. Our drug testing policy guide covers medical necessity and codes.
• Add it to the credential file. Plans ask for the CLIA certificate in facility credentialing; it's on our credentialing documents checklist.

Renewal and changes

• Every two years. The certificate renews when you pay the next fee coupon, which CMS emails ahead of the expiration date. A missed coupon means a lapsed certificate, which means you can't test, and claims for tests on those dates deny.
• Keep your email current with the state agency. With paper coupons gone, a stale email address is the most common way a certificate lapses.
• Report changes to the state agency: a new name, address, director, ownership or test list. Ask the agency for its timeframe and form, and don't move testing to a new address before the change is approved.
• Put it on the compliance calendar. We track CLIA every two years alongside DEA registrations every three years, licenses and insurance, with a reminder 90 days ahead. Comply's compliance calendar has the full list of recurring dates.

Running waived tests the right way

A Certificate of Waiver doesn't mean "no rules." It means you must follow the manufacturer's instructions exactly. From the drug screening policy we write for programs:

• Follow the package insert exactly, including the read time; never alter the test.
• Check expiration dates and storage temperatures, and run quality controls as the manufacturer directs, with a log.
• Train each person who tests and document their competency before they test alone, then each year.
• Record each result, the device lot number and who read it.
• Treat a positive instant result as presumptive until a lab confirms it, when the result will change care or the client disputes it.
• The clinical director keeps the certificate current, checks competency records and reviews testing patterns each quarter.

Surveyors ask to see this: in a mock survey we pull the CLIA certificate, the QC log, the competency records and a sample of results against the package insert. Joint Commission programs can compare with Comply's Joint Commission behavioral health checklist.

Already open and just need the certificate or a testing policy? Consulting by the hour is $175 per hour, or book a free 30-minute call.

Questions

Do I need a CLIA waiver to use urine drug test cups?

Yes, if you read the results on site and use them in a client's care. Cups the FDA lists as waived need a Certificate of Waiver for the testing location. If you only collect specimens and send them to a lab, the lab's certificate covers the testing.

How much does a CLIA certificate of waiver cost?

As of 2026, $248 for two years, paid online through pay.gov when the fee coupon arrives by email. CMS adjusts CLIA fees every two years, so check the amount on your coupon.

How long is a CLIA waiver good for?

Two years. It renews when you pay the next fee coupon, which is now sent only by email, so keep the email address on file current.

Where do I send form CMS-116 in Texas?

To the Texas CLIA state agency, with HHSC's Form 3225 supplement. CMS says email is preferred. HHSC's form lists Health Facility Compliance ([email protected]) for questions; confirm the current submission address with them before you send.

Does each office need its own CLIA waiver?

Generally yes. 42 CFR 493.35 requires a separate application for each location, with narrow exceptions for mobile or temporary sites, limited public health testing by nonprofits or governments, and hospital campuses.

Why are our Texas Medicaid drug test claims denying?

For dates of service from June 1, 2026, Medicaid plans deny lab procedure codes when the CLIA certificate in your PEMS enrollment doesn't cover them. Check that your CLIA number and certificate type are in PEMS and match the claim.

Sources

• CMS, CLIA program; Form CMS-116; certification quick start guide; paperless and pay.gov FAQ
• eCFR, 42 CFR Part 493 and section 493.35 (certificate of waiver, multiple sites)
• Federal Register, CLIA fees final rule, CMS-3326-F (December 28, 2023); Minnesota Department of Health, CLIA fee schedule
• Texas HHSC, Form 3225, Supplement to CMS-116
• FDA, CLIA test categorization database
• CMS, MLN MM13253, new waived tests and the QW modifier
• Community Health Choice, revised implementation timeframes of CLIA certification data (HHSC's Texas Medicaid edit timeline); TMHP, PEMS licenses