CPT code 81229: Chromosomal microarray, copy number and SNP analysis2026 Medicare lab fee · Clinical Laboratory Fee Schedule
Genome-wide SNP microarray analysis evaluates constitutional chromosomal copy-number changes and SNP patterns, commonly during evaluation of developmental delay or congenital anomalies.
Medicare pays $1,160.00 for 81229 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
$1,160.00
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 8 sections
What 81229 covers
This genome-wide cytogenomic assay uses comparative genomic hybridization microarray analysis together with SNP interrogation to assess constitutional chromosomal abnormalities. It evaluates copy-number changes across the genome and SNP patterns, rather than examining only one named gene or a selected chromosomal region. Genetics, pediatrics, and other clinicians may order it when evaluating unexplained developmental delay, intellectual disability, or multiple congenital anomalies. A clinical genetics laboratory performs the analysis on DNA from the patient specimen.
Report 81229 for the genome-wide assay, not separately for individual findings or probes. Medicare pays it through the CLFS only. The 2026 national CLFS amount is $1,160.00, unchanged from 2020 through 2026; the same amount applies across states and localities, without an office or facility difference. Payment is per code, and the code has no physician-fee-schedule payment.
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 81229
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 81229. 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 81229 with status X (excluded by statute), so the test itself is paid only from the CLFS.
81229 on the lab fee schedule since 2020
81229 · CLFS 2026 Q4 (current)
$1,160.00
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.
81229 compared with similar tests
- 81228Chromosomal microarrayCGH copy-number analysis$900.00
- Choose 81229 when the assay includes SNP interrogation as well as genome-wide copy-number analysis. 81228 is the related CGH microarray code without the SNP component.
- 88262Chromosome analysis15–20 cells, two karyotypes$125.49
- 88262 is chromosome analysis by karyotyping. Use 81229 for genome-wide microarray assessment of copy number and SNP patterns.
- 88271DNA probeEach probe$21.42
- 88271 reports molecular cytogenetic DNA-probe testing, generally directed at a selected region. 81229 is the genome-wide microarray assay.
81229 billing questions
How does 81229 differ from 81228?
81229 includes SNP interrogation alongside genome-wide copy-number analysis. 81228 describes the related comparative genomic hybridization microarray analysis without the SNP component.
Is 81229 reported per finding or per probe?
Report the code for the genome-wide assay performed, not separately for each probe, copy-number change, or SNP result.
What clinical situations commonly prompt this test?
It is commonly ordered during evaluation of unexplained developmental delay, intellectual disability, or multiple congenital anomalies when a genome-wide assessment of constitutional chromosomal abnormalities is needed.
Does Medicare pay 81229 under the physician fee schedule?
No. Medicare pays this test through the CLFS only, using one national amount across localities and care settings.
Should a targeted FISH test be reported instead?
Use a targeted molecular cytogenetic probe assay when the clinical question concerns a selected chromosomal region. 81229 is the genome-wide copy-number and SNP microarray assay.
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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