CPT code 88249: Chromosome breakage test, 100 cells, clastogen stress2026 Medicare lab fee · Clinical Laboratory Fee Schedule
Clastogen-stress chromosome analysis scores 100 cells to evaluate chromosome breakage associated with genetic defects in a laboratory study.
Medicare pays $173.17 for 88249 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
$173.17
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 8 sections
What 88249 covers
Code 88249 identifies chromosome analysis performed under clastogen stress to evaluate genetic chromosome defects. The laboratory assesses chromosome findings after clastogen exposure and scores 100 cells. A cytogenetics laboratory performs and reports the analysis; the results support clinical assessment of chromosome-breakage defects.
Report 88249 for the clastogen-stress analysis when 100 cells are scored; it is distinct from chromosome-analysis services with other stated scoring ranges. Medicare pays the test through the CLFS, which uses one national amount across states and localities without geographic or office-versus-facility adjustment. The 2026 national CLFS amount is $173.17, unchanged from 2020 through 2026. The test is paid only under the CLFS, not the physician fee schedule.
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 88249
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 88249. 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 88249 with status X (excluded by statute), so the test itself is paid only from the CLFS.
88249 on the lab fee schedule since 2020
88249 · CLFS 2026 Q4 (current)
$173.17
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.
88249 compared with similar tests
- 88245SCE analysisBaseline, 20–25 cells$173.17
- 88249 is clastogen-stress analysis with 100 cells scored; 88245 has a 20–25-cell scoring range.
- 88248Breakage analysisBaseline, 50–100 cells$173.17
- 88249 identifies clastogen-stress analysis with 100 cells scored. 88248 has a 50–100-cell scoring range.
- 88261Chromosome analysisFive-cell count$264.34
- 88261 has a five-cell scoring level. 88249 is the clastogen-stress analysis with 100 cells scored.
88249 billing questions
When is 88249 appropriate instead of routine chromosome analysis?
Use 88249 for clastogen-stress chromosome analysis with 100 cells scored. Other chromosome-analysis codes represent different scoring ranges or study types.
How does 88249 differ from 88248?
88249 identifies clastogen-stress analysis with 100 cells scored. 88248 is a chromosome-analysis code with a 50–100-cell range.
What cell count does 88249 represent?
It represents clastogen-stress analysis with 100 cells scored. The laboratory documentation should support the service and count.
How does Medicare pay for 88249?
Medicare pays it through the CLFS using one national amount across localities, with no office-versus-facility adjustment. The test is paid only under the CLFS.
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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