CPT code 87046: Stool culture, additional pathogens, per plate2026 Medicare lab fee · Clinical Laboratory Fee Schedule
Aerobic stool culture isolates and presumptively identifies additional bacterial pathogens beyond the routine stool culture, reported by plate.
Medicare pays $9.44 for 87046 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
$9.44
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 87046 covers
87046 is used for aerobic stool culture aimed at recovering pathogens beyond those sought in the routine stool culture. A clinical microbiology laboratory performs the culture on stool when additional enteric bacterial pathogens are being sought; the work includes isolation and presumptive identification of isolates. The result supports evaluation of suspected bacterial enteric infection.
Report 87046 with 87045 when the laboratory performs additional-pathogen culture work, counting one unit for each plate. Documentation should identify the stool culture work and support the plate count. Medicare pays this test through the CLFS, with one national amount across states and localities and no office-versus-facility rate difference. The 2026 national CLFS amount is $9.44, unchanged since 2020. Payment is through the CLFS only.
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 87046
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 87046. 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 87046 with status X (excluded by statute), so the test itself is paid only from the CLFS.
87046 on the lab fee schedule since 2020
87046 · CLFS 2026 Q4 (current)
$9.44
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.
87046 compared with similar tests
- 87045Stool cultureAerobic, Salmonella and Shigella$9.44
- 87045 describes the routine aerobic stool culture. Use 87046 for additional-pathogen culture work, counted by plate, alongside the routine service.
- 87070Aerobic cultureNon-urine, blood, or stool$8.62
- 87070 describes aerobic culture of other specimen types. Use 87046 for additional-pathogen aerobic culture work on stool.
- 87077Aerobic identificationDefinitive identification, each isolate$8.08
- 87046 covers additional stool culture with presumptive identification; 87077 describes further identification of an aerobic bacterial isolate.
- 87040Blood cultureBacterial culture$10.32
- 87040 is for bacterial blood culture. 87046 is for additional-pathogen aerobic culture from stool.
87046 billing questions
When should 87046 be reported with 87045?
Report 87045 for the routine aerobic stool culture. Add 87046 when the laboratory performs culture work for additional pathogens, with the unit count based on the plates used.
Does 87046 include definitive identification of an isolate?
It covers isolation and presumptive identification. Further aerobic isolate identification may be reported with 87077 when that additional work is performed and documented.
How are units determined for 87046?
Report one unit for each plate used for additional-pathogen culture work. The laboratory documentation should support the plate count.
Can 87046 be reported for a non-stool specimen?
No. 87046 is for additional-pathogen aerobic culture work on stool; 87070 describes aerobic culture of other specimen types.
How does Medicare pay for 87046?
Medicare pays the service through the CLFS at one national amount, with the same rate across localities and care settings. Payment is through the CLFS only.
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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