CPT code 81540: Tumor classifier, 92-gene mRNA assay2026 Medicare lab fee · Clinical Laboratory Fee Schedule
A 92-gene tumor tissue expression profile estimates the likely cancer type and subtype when the primary site remains unknown.
Medicare pays $3,750.00 for 81540 under the 2026 Clinical Laboratory Fee Schedule: one national amount, the same in every state and setting.
Medicare lab fee · CLFS 2026 Q4
National CLFS amount
$3,750.00
In effect since Jan 1, 2026. The same amount in every state, payment locality and setting.
- Geographic adjustment
- None
- Office vs facility
- Same
- Since 2020
- Unchanged
- CMS updates
- Quarterly
Medicare pays the lesser of the lab’s charge and this amount. Patients usually owe no Part B deductible or coinsurance for covered clinical lab tests.
On this page 7 sections
What 81540 covers
This assay analyzes gene-expression patterns in tumor tissue to estimate the cancer's main type and subtype when the primary site is unknown. It uses formalin-fixed, paraffin-embedded tissue and real-time RT-PCR to assess 92 genes, including content and housekeeping genes; an algorithm reports probabilities for the predicted classification. Oncologists may order the profile after a malignancy is identified but its origin remains unclear, and a molecular laboratory performs the testing. Results are considered with the clinical and pathologic findings.
Report 81540 for the tumor-of-unknown-origin profile as a complete assay, rather than separately reporting its individual gene measurements. Medicare pays the test through the CLFS, with one national amount across localities and no office-versus-facility adjustment. The 2026 national CLFS amount is $3,750 and has remained unchanged since 2020. The physician fee schedule excludes the test by statute; payment is through the CLFS.
This summary was written with AI assistance from CMS Clinical Laboratory Fee Schedule data. Amounts on this page come directly from CMS files.
How Medicare pays 81540
Clinical lab tests aren’t priced like physician services. They’re paid from their own fee schedule, with its own rules. See the whole lab fee schedule.
One national amount
CMS sets a single Clinical Laboratory Fee Schedule amount for 81540. There’s no geographic (GPCI) adjustment, so it pays the same in every state and payment locality.
No office or facility rate
Lab tests aren’t built from relative value units, so there’s no office and facility split: the place of service doesn’t change the CLFS amount.
Updated every quarter
CMS republishes the CLFS each quarter. New tests, often proprietary laboratory analyses (PLA codes), join during the year; existing amounts are updated each January.
Excluded from the physician fee schedule
The physician fee schedule lists 81540 with status X (excluded by statute), so the test itself is paid only from the CLFS.
81540 on the lab fee schedule since 2020
81540 · CLFS 2026 Q4 (current)
$3,750.00
Unchanged since Jan 1, 2020
27 quarterly CLFS releases on file, first CLFS 2020 Q1. A code missing from a quarter wasn’t on that release.
81540 compared with similar tests
- 81538Lung survival assaySerum protein signature$2,871.00
- 81540 classifies a tumor when its primary site is unknown; 81538 is an oncology assay focused on lung cancer.
- 81529Melanoma assay31-gene mRNA analysis$7,193.00
- 81540 predicts a likely cancer type and subtype for a tumor of unknown origin. 81529 is a 31-gene mRNA assay for cutaneous melanoma.
- 81524CNS tumor assayMethylation-based classificationNo national amount
- 81540 uses mRNA expression analysis for tumor-of-origin classification. 81524 is a CNS tumor assay using DNA methylation analysis.
81540 billing questions
When is 81540 the appropriate tumor profiling code?
Use it for the 92-gene expression classifier that predicts a likely cancer type and subtype when the tumor's primary site is unknown. A profile directed at a named cancer may have a different code.
What tissue and method does this assay use?
It analyzes formalin-fixed, paraffin-embedded tumor tissue using real-time RT-PCR to assess gene expression.
Are the 92 genes billed as separate units?
No. The genes are components of the tumor-of-origin profile, not 92 separately reported gene tests.
Does Medicare pay 81540 under the physician fee schedule?
No. The test is paid through the CLFS, with one national amount applying across localities and settings.
What documentation supports reporting 81540?
Document that the tested malignancy's primary site is unresolved and that the tumor-of-origin expression profile was performed.
Where this amount comes from
FeeBase reads lab amounts directly from the CMS Clinical Laboratory Fee Schedule file for the quarter: one row per code, with its payment indicator and national amount. Contractor-priced tests are labeled, never given a made-up amount. Amounts are Medicare payment limits, not a patient’s bill or a commercial rate.
CMS CLFS 2026 Q4 · effective Oct 1, 2026 through the day before Jan 1, 2027
Show the CMS file line behind this amount
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