Medical Billing • CPT Modifiers • Laboratory Billing

Modifier 90

Reference (Outside) Laboratory

Learn what Modifier 90 means, when it is used, who reports it, how referred laboratory services are billed, CLIA requirements, common denials, AR investigation steps and practical billing examples.

Start Learning Quick Cheat Sheet

Reference / Outside Laboratory

Modifier 90 at a Glance

The essential points every medical biller, coder and AR caller should know.

Modifier 90

Identifies a laboratory service that was performed by a reference or outside laboratory.

LAB

Laboratory Referral

The billing laboratory refers the test to another laboratory for performance.

CLIA

CLIA Information

Applicable CLIA information for the performing laboratory must be reported according to Medicare claim requirements.

Denial Management

Incorrect use of Modifier 90 can result in unprocessable claims, payment issues or laboratory billing denials.

What Is Modifier 90?

Understanding reference laboratory billing.

Simple Definition

Modifier 90 is used to identify a laboratory service that was performed by a laboratory other than the laboratory submitting the claim.

In a typical referred-laboratory arrangement, one laboratory receives the test order and billing responsibility while another laboratory actually performs the test.

CMS uses Modifier 90 to identify referred laboratory tests on the claim line.

Easy Way to Remember

Think:

“90 = The lab billed it, but another lab performed it.”

The modifier identifies the referred test. It does not mean the patient was physically sent somewhere for an office visit.

How Reference Laboratory Billing Works

Follow the service from the ordering provider to the billing and performing laboratories.

1 A provider orders a laboratory test for the patient.

2 The patient provides the specimen to the laboratory or collection location.

3 The billing laboratory determines that another laboratory will perform the test.

4 The specimen/test is referred to the outside reference laboratory.

5 The reference laboratory performs the laboratory test.

6 The billing laboratory reports the referred service with Modifier 90 when applicable.

7 Required performing/reference laboratory information is reported on the claim.

8 The payer processes the claim under the applicable laboratory billing rules.

Who Uses Modifier 90?

Modifier 90 is primarily associated with the billing of referred laboratory services.

BILL

Billing Laboratory

The laboratory responsible for billing the referred service may report Modifier 90 on the applicable service line.

REF

Reference Laboratory

The outside laboratory performs the referred laboratory test. The applicable performing-laboratory information must be reported according to claim requirements.

CMS

Medicare Rules

Medicare has specific requirements for referred laboratory services, including reporting the applicable CLIA information.

Important Medicare Point

CMS states that referral laboratory claims are permitted for independently billing clinical laboratories with specialty code 69 under the referenced Medicare claims-processing guidance.

Modifier 90: Referred vs Self-Performed

This distinction is critical when reviewing laboratory claims.

Situation	Who Performs Test?	Modifier 90?	Basic Concept
Self-performed	Billing laboratory	Generally no	Billing laboratory performed the test itself.
Referred test	Outside/reference laboratory	Yes, when applicable	Billing laboratory refers the test to another laboratory.
Mixed laboratory claim	Billing laboratory + reference laboratory	On referred service line	Self-performed tests and referred tests may require different line-level reporting.
Reference laboratory directly bills Medicare	Reference laboratory	Depends on billing arrangement	Verify which laboratory is actually submitting the claim.

AR Tip

Never determine Modifier 90 only from the CPT code. First determine who billed the service and who actually performed the test.

Modifier 90 and CLIA

CLIA reporting is an important part of Medicare laboratory claim processing.

What Is CLIA?

CLIA stands for the Clinical Laboratory Improvement Amendments.

CLIA establishes quality standards for laboratory testing performed on human specimens.

For Medicare laboratory billing, applicable CLIA information must be reported according to CMS claim-processing requirements.

For Referred Tests

CMS guidance states that when a billing laboratory refers a test to another laboratory, the CLIA number of the laboratory where the testing is rendered must be reported on the claim.

This is one of the most important claim-data elements to verify when investigating a Modifier 90 issue.

Modifier 90 on Electronic Claims

CMS provides specific reporting requirements for referred laboratory services.

837

Claim Format

Electronic laboratory claims use the applicable HIPAA X12N 837 claim format.

Service Line

Modifier 90 identifies the referred laboratory service at the line-item level.

CLIA

Reference CLIA

The CLIA number of the laboratory where the testing was performed is reported according to CMS requirements.

CMS Electronic Claim Guidance

CMS states that for electronic claims involving referred laboratory services, Modifier 90 identifies the referral tests and the reference laboratory’s CLIA number is reported in the appropriate electronic claim loop.

Modifier 90 on CMS-1500

Key claim elements to review for referred laboratory services.

CMS-1500 Area	What to Verify	Why It Matters
Item 24D	CPT/HCPCS and applicable modifier	Modifier 90 identifies the referred service line.
Item 23	Applicable CLIA number	Medicare requires CLIA information for applicable laboratory services.
Item 32	Performing/reference laboratory information	Identifies where the laboratory service was actually performed.
Billing Provider	Billing laboratory information	Establishes which entity submitted the claim.

CMS Paper Claim Guidance

CMS guidance states that when the referring laboratory is the billing laboratory, the reference laboratory’s name and address are reported in Item 32 and the reference laboratory’s CLIA number is reported in Item 23 for the applicable referred laboratory service.

Modifier 90 Billing Examples

Practical examples for billers and AR callers.

Example 1 — Test Referred

Laboratory ABC receives a specimen but does not perform the required specialty test. ABC sends the test to Laboratory XYZ.

CPT + 90

The applicable Medicare claim identifies the service as a referred test and reports the required reference laboratory information.

Example 2 — Self-Performed Test

Laboratory ABC receives the specimen and performs the test within its own laboratory.

CPT

Modifier 90 would generally not be appropriate simply because the test is a laboratory service.

Example 3 — Mixed Services

Laboratory ABC performs a CBC itself but sends a specialized tissue test to Laboratory XYZ.

CBC — CPT Specialty Test — CPT + 90

The referred test line is identified separately from the self-performed test.

Example 4 — Missing Reference CLIA

The billing laboratory reports Modifier 90 but fails to provide the applicable performing laboratory CLIA information.

CPT + 90

The claim may become unprocessable or require correction, depending on the payer’s processing rules.

Example 5 — Wrong Laboratory Information

Modifier 90 is reported, but the claim identifies the wrong laboratory as the performing laboratory.

CPT + 90

Verify the actual performing laboratory, NPI, address and applicable CLIA information.

Example 6 — Reference Lab Bills Directly

The reference laboratory itself submits the claim rather than the referring laboratory.

Verify Billing Arrangement

Do not automatically apply Modifier 90. First determine who is the actual billing entity and verify the payer’s rules.

Common Modifier 90 Denials

Common denial and claim-processing problems for referred laboratory services.

Denial 01

Missing Modifier 90

A referred laboratory service was billed without the required Modifier 90.

Denial 02

Incorrect Modifier 90

Modifier 90 was appended even though the billing laboratory performed the test itself.

Denial 03

Missing CLIA

Required CLIA information for the performing laboratory was missing or invalid.

Denial 04

Wrong Performing Lab

The claim reports incorrect reference laboratory information.

Denial 05

Unprocessable Claim

Required billing, performing laboratory or CLIA information was not reported correctly.

Denial 06

Duplicate Billing

Both the referring and reference laboratories may have billed the same service when only one billing arrangement was permitted.

Denial 07

Wrong Billing Entity

The entity submitting the claim does not match the applicable Medicare laboratory billing requirements.

Denial 08

Laboratory Not Eligible

The billing or performing laboratory does not meet the applicable payer or laboratory requirements.

Denial 09

Payer Policy Conflict

The payer has a specific reference-laboratory billing rule that differs from the submitted claim.

AR Caller Workflow for Modifier 90 Denials

A practical denial-management workflow.

Review ERA / EOB

Identify the exact denial message, CARC, RARC, adjustment amount and affected laboratory claim line.

Identify CPT / HCPCS

Determine the exact laboratory test that was denied.

Identify Billing Laboratory

Determine which laboratory actually submitted the claim.

Identify Performing Laboratory

Confirm which laboratory actually performed the laboratory test.

Verify Modifier 90

Determine whether the test was referred and whether Modifier 90 was correctly reported.

Verify CLIA

Confirm the performing laboratory’s CLIA number and the claim reporting requirements.

Verify NPI and Address

Confirm the reference laboratory’s name, address and NPI as applicable to the claim format.

Check Billing Arrangement

Determine whether the referring laboratory or reference laboratory is responsible for billing the payer.

Check Payer Policy

Review Medicare, MAC, Medicaid, Medicare Advantage or commercial payer requirements.

Determine Root Cause

Identify whether the issue is modifier, CLIA, provider, billing entity, duplicate billing or documentation-related.

Correct or Appeal

Submit the appropriate corrected claim or appeal based on the verified root cause.

Document Follow-Up

Record payer instructions, reference number, representative name, filing deadline and next action.

AR Caller Script for Modifier 90

Questions to ask the payer when investigating a referred laboratory denial.

“I’m calling regarding a laboratory claim that was denied involving Modifier 90.”

“Could you please provide the exact denial reason and the applicable CARC and RARC codes?”

“Can you confirm whether the denial is related to Modifier 90?”

“Can you confirm whether this laboratory test is considered a referred laboratory service under your policy?”

“Can you confirm whether the billing laboratory is permitted to bill this referred service?”

“Can you confirm what CLIA information is required for the performing laboratory?”

“Can you confirm whether the performing laboratory’s NPI and address are required on the claim?”

“Was the claim denied because the reference laboratory information was missing or incorrect?”

“Does your payer require the reference laboratory’s name and address in a specific CMS-1500 or electronic claim field?”

“If we submit a corrected claim, could you please confirm the exact correction required and the filing deadline?”

“May I have the call reference number for our records?”

Modifier 90 Documentation & Claim Checklist

Test Ordered

Confirm the laboratory test ordered by the treating provider.

Billing Laboratory

Identify the laboratory submitting the claim.

Performing Laboratory

Identify the laboratory that actually performed the test.

CLIA Number

Verify the applicable CLIA number for the laboratory performing the test.

NPI

Verify the applicable billing and performing laboratory NPI information.

Address

Confirm the performing laboratory’s name and address.

Root Causes of Modifier 90 Denials

Missing Modifier

The referred service was billed without Modifier 90.

Incorrect Modifier

Modifier 90 was reported when the billing laboratory actually performed the test.

Missing CLIA

Required CLIA information was missing or incorrect.

Wrong NPI

The claim identifies the wrong performing laboratory NPI.

Wrong Address

Performing laboratory information does not match the actual testing location.

Duplicate Billing

More than one laboratory billed the same referred test.

Wrong Billing Entity

The entity submitting the claim does not meet applicable referred-laboratory billing rules.

Payer Rule

The payer applies additional reference-laboratory requirements.

Modifier 90 and Medicare

Medicare Checklist

Identify the laboratory CPT/HCPCS code.
Determine whether the test was referred.
Identify the billing laboratory.
Identify the performing/reference laboratory.
Verify Modifier 90.
Verify the reference laboratory CLIA number.
Verify applicable NPI and address information.
Confirm the billing arrangement.

CMS Guidance

CMS states that independent laboratories may submit claims for referred laboratory services and that Modifier 90 identifies the referred laboratory service.

CMS also requires applicable information identifying the performing/reference laboratory and its CLIA number on referred laboratory claims.

Medicare Laboratory Resources

Important CMS resources for laboratory billing research.

CLFS

Clinical Laboratory Fee Schedule

CMS publishes Medicare payment information for most clinical diagnostic laboratory tests through the CLFS.

DOS

Laboratory Date of Service

CMS maintains specific laboratory date-of-service policies and exceptions.

CLIA

Clinical Laboratory Information

CMS provides a dedicated Clinical Labs Information Center with Medicare laboratory resources.

2026 CMS Laboratory Updates

CMS’s current 2026 Clinical Laboratory Fee Schedule resources contain quarterly files and current laboratory payment information. CMS also states that inclusion of a laboratory code or payment amount does not itself establish Medicare coverage.

Modifier 90 and Medicaid

Medicaid Review Checklist

Identify the state Medicaid program.
Verify whether Modifier 90 is recognized.
Review the state Medicaid laboratory billing manual.
Verify CLIA requirements.
Verify reference laboratory requirements.
Check Medicaid MCO requirements.
Verify billing laboratory enrollment.

Do Not Assume Medicare Rules

Medicaid rules can differ by state. Medicaid managed care organizations can also establish additional billing and claim requirements.

Always verify the applicable state Medicaid or MCO policy before correcting or appealing a Modifier 90 denial.

Modifier 90 and Commercial Insurance

Verify Payer Policy

Confirm whether the payer recognizes Modifier 90 and how it should be reported.

Verify Billing Entity

Determine which laboratory is permitted to submit the claim.

Verify CLIA

Confirm whether the payer requires performing laboratory CLIA information.

Verify NPI

Confirm billing and performing laboratory identifiers.

Check Duplicate Billing

Determine whether both laboratories submitted the same service.

Verify Appeal Rules

Follow the payer’s current corrected-claim and appeal requirements.

How to Prevent Modifier 90 Denials

Identify Performing Lab

Confirm where the test was actually performed before billing.

Verify Modifier

Use Modifier 90 only when the service qualifies as a referred laboratory service under the payer’s rules.

Verify CLIA

Confirm the correct performing laboratory CLIA information.

Verify NPI

Maintain accurate billing and performing laboratory identifiers.

Prevent Duplicate Billing

Establish clear billing responsibility between referring and reference laboratories.

Audit Denials

Track Modifier 90 denials by payer, laboratory, CPT and root cause.

      
        Modifier 90 Quick Cheat Sheet
      
        Modifier 90 identifies a referred laboratory service.
      
        The billing laboratory and performing laboratory can be
        different entities.
      
        Do not use Modifier 90 merely because a service is a laboratory
        test.
      
        First determine who actually performed the test.
      
        Verify who is responsible for billing the payer.
      
        For Medicare referred laboratory claims, verify applicable CLIA
        reporting requirements.
      
        Verify the performing/reference laboratory’s name and address.
      
        Verify the applicable NPI information.
      
        Check for duplicate billing between referring and reference
        laboratories.
      
        Verify payer-specific reference-laboratory requirements.
      
        Modifier 90 does not guarantee payment.
      
        Always investigate the actual denial reason before correcting the
        claim.

      
        Before You Bill Modifier 90
      
        Confirm the test was actually referred.
      
        Identify the billing laboratory.
      
        Identify the performing/reference laboratory.
      
        Verify the CPT/HCPCS code.
      
        Verify Modifier 90.
      
        Verify the performing laboratory CLIA number.
      
        Verify NPI and address information.
      
        Confirm the billing arrangement.
      
        Check payer-specific laboratory policy.
      
        Check for duplicate billing.
      
        Confirm the claim is submitted with the required laboratory
        information.
      
        Track the claim after submission.

Modifier 90 FAQs

What is Modifier 90?

Modifier 90 identifies a laboratory service that was referred to and performed by an outside/reference laboratory.

What does Modifier 90 mean in medical billing?

It indicates that the laboratory service was performed by another laboratory rather than the laboratory billing the service.

Is Modifier 90 used for an outside laboratory?

Yes. Modifier 90 is commonly described as the reference or outside laboratory modifier because it identifies a referred laboratory service.

Who bills Modifier 90?

Under Medicare’s referred laboratory rules, the billing laboratory reports Modifier 90 on the applicable referred service line when required.

Does Modifier 90 mean the test was performed at another location?

Not necessarily in the everyday sense of the phrase. The key issue is that another laboratory performed the referred laboratory service.

Should Modifier 90 be used when the laboratory performs the test itself?

Generally no. Modifier 90 is intended to identify referred laboratory services, not self-performed laboratory tests.

Is Modifier 90 required for Medicare referred laboratory services?

CMS guidance states that independent laboratories use Modifier 90 to identify referred laboratory services, and a referred laboratory claim without the modifier may be returned as unprocessable when the service can be identified as referred.

What is the CLIA requirement for Modifier 90?

For Medicare referred laboratory claims, CMS requires the applicable CLIA information for the laboratory where the test was actually performed.

Where is the CLIA number reported on a CMS-1500 claim?

CMS guidance for paper referred laboratory claims identifies Item 23 for the applicable reference laboratory CLIA number.

Where is the reference laboratory information reported?

CMS guidance for paper claims identifies Item 32 for the reference laboratory’s name and address when the referring laboratory is the billing laboratory.

Can Modifier 90 be used with any CPT laboratory code?

Modifier 90 should not be appended automatically to every laboratory CPT code. The actual service must meet the applicable referred-laboratory billing requirements.

What is the difference between Modifier 90 and Modifier 91?

Modifier 90 identifies a referred laboratory service performed by another laboratory. Modifier 91 is associated with repeat clinical diagnostic laboratory testing on the same day to obtain additional results.

What is the difference between Modifier 90 and Modifier 59?

Modifier 90 concerns the laboratory performing the referred service. Modifier 59 identifies a distinct procedural service under applicable coding rules. They address completely different billing concepts.

Why was my Modifier 90 claim denied?

Common causes include missing Modifier 90, incorrect use of the modifier, missing CLIA information, incorrect performing laboratory information, duplicate billing or payer-specific laboratory requirements.

Can both laboratories bill the same test?

Do not assume that both laboratories can bill the same service. Medicare has specific rules concerning which laboratory may bill a referred laboratory service. CMS states that only one laboratory may bill Medicare for the referred service under the applicable referred-lab rules.

What should an AR caller check first?

Start with the ERA/EOB denial reason, then identify the CPT, billing laboratory, performing laboratory, Modifier 90, CLIA information and payer-specific requirements.

Does Modifier 90 guarantee payment?

No. Modifier 90 identifies the referred service but does not override coverage, medical necessity, laboratory eligibility, CLIA or payer-specific billing requirements.

Does Medicare have current laboratory fee schedule information?

Yes. CMS maintains the Clinical Laboratory Fee Schedule and publishes current quarterly files.

Where can I find official CMS laboratory resources?

CMS maintains a Clinical Labs Information Center containing Medicare laboratory billing, CLFS, CLIA, NCCI and other laboratory resources.

Official CMS References

Use official CMS resources when validating Modifier 90 and laboratory billing requirements.

CMS — Referred Laboratory Services / Modifier 90 Guidance CMS guidance covering referred laboratory services, Modifier 90, CLIA information and electronic claim reporting. CMS — Medicare Claims Processing Manual, Chapter 16 Laboratory services guidance covering referred laboratory claims and Modifier 90. CMS — Clinical Labs Information Center Official CMS laboratory billing, CLIA, Medicare and coding resources. CMS — Clinical Laboratory Fee Schedule Current Medicare clinical laboratory fee schedule information. CMS — Laboratory Date of Service Policy Current CMS laboratory date-of-service policy and applicable exceptions. CMS — Medicare NCCI Policy Manual Current Medicare NCCI policy reference.

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