CPT code 81301: MSI analysis, mismatch repair markers2026 Medicare lab fee · Clinical Laboratory Fee Schedule
Microsatellite instability analysis evaluates neoplastic tissue markers for mismatch repair deficiency and supports assessment for Lynch syndrome.
Medicare pays $348.56 for 81301 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
$348.56
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 81301 covers
81301 reports laboratory analysis of microsatellite markers in neoplastic tissue to assess mismatch repair deficiency. It is used in evaluating Lynch syndrome, also called hereditary nonpolyposis colorectal cancer. The analysis may compare neoplastic tissue with normal tissue when performed. Molecular pathology laboratories perform or report this analysis. It evaluates tumor microsatellite instability rather than sequencing or testing a specific inherited cancer-predisposition gene. The finding supports assessment of mismatch repair status in the tested neoplasm.
Medicare pays 81301 only under the CLFS; it is excluded from the physician fee schedule. The 2026 national CLFS amount is $348.56, unchanged since 2020. CMS sets one amount per code for every state and locality, with no geographic adjustment or office-versus-facility difference.
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 81301
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 81301. 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 81301 with status X (excluded by statute), so the test itself is paid only from the CLFS.
81301 on the lab fee schedule since 2020
81301 · CLFS 2026 Q4 (current)
$348.56
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.
81301 compared with similar tests
- 81317PMS2 sequencingFull gene sequence$676.50
- 81317 analyzes the PMS2 gene sequence. 81301 evaluates microsatellite markers in neoplastic tissue for mismatch repair deficiency.
- 81318PMS2 testingKnown familial variants$331.00
- 81318 tests for known familial PMS2 variants; 81301 evaluates microsatellite instability in neoplastic tissue.
- 81319PMS2 analysisDuplication and deletion variants$203.50
- 81319 analyzes PMS2 gene duplications or deletions. 81301 evaluates microsatellite markers for mismatch repair deficiency.
81301 billing questions
What does 81301 analyze?
It analyzes microsatellite markers in neoplastic tissue to assess mismatch repair deficiency. The analysis may include comparison with normal tissue when performed.
How is 81301 different from PMS2 testing?
81301 evaluates microsatellite instability in neoplastic tissue. PMS2 codes address analysis of the PMS2 gene, including sequence analysis, known familial variants, or duplications and deletions.
Does the analysis include comparison with normal tissue?
It may include comparison of neoplastic and normal tissue when performed.
Does Medicare payment vary by locality or setting?
No. Medicare pays 81301 under the CLFS at one national amount, with no geographic or office-versus-facility adjustment.
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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