How much does Medicare pay for CPT 81301?

Medicare allowed an average of $341.38 per service and paid $341.38 of that, the balance being the patient's coinsurance and deductible (2024 data). Providers submitted an average of $488.69, which is what they billed rather than what they received — Medicare pays its fee schedule regardless of the charge.

What is CPT code 81301?

Microsatellite instability analysis. It was billed 3,208 times to 2,965 Medicare beneficiaries by 20 providers in 2024.

Does 81301 pay differently in an office than a hospital?

Yes. The allowed amount averaged $341.38 in an office setting and $340.67 in a facility. The office rate is generally higher because the practice supplies the room, staff and equipment out of that single payment; in a hospital those are billed separately by the facility.

Which specialty bills 81301 most?

Clinical Laboratory, with 3,164 services from 17 clinicians. Next are Pathology.

CPT 81301

Microsatellite instability analysis

$341.38Medicare-allowed amount per service, averaged across 3,208 services

Providers submitted

$488.69

Asking price, not received

Medicare allowed

$341.38

The fee schedule figure

Medicare paid

$341.38

Balance is patient coinsurance

Providers submitted an average of $488.69 for this code and Medicare allowed $341.38 — 1.4× less. That gap is normal and means nothing on its own: Medicare pays its fee schedule regardless of what is billed, so the submitted figure describes a hospital chargemaster, not a price anyone paid. Of the allowed amount Medicare paid $341.38 (100%); the rest is the patient’s coinsurance and deductible.

Office pays differently to hospital

Office / non-facility: $341.38
Hospital / facility: $340.67

The office rate is higher because the practice supplies the room, staff and equipment out of that payment. In a hospital the facility bills those separately, so the clinician's share is smaller — the total cost to Medicare is usually higher, not lower. 3,176 services were billed in an office setting and 32 in a facility.

Services: 3,208
Beneficiaries: 2,965
Providers billing it: 20
Total allowed: $1,095,147

What Medicare pays for CPT 81301

Across 3,208 services billed by 20 providers to 2,965 beneficiaries, Medicare allowed an average of $341.38 per service. The allowed amount is the figure that matters: it is what Medicare and the patient together owe, set by the fee schedule and adjusted for local practice costs. What a provider chose to submit has no bearing on it.

Who bills 81301

Specialty	Services	Beneficiaries	Avg allowed	Providers
Clinical Laboratory	3,164	2,921	$341.38	17
Pathology	44	44	$340.92	3

81301 reimbursement by state

Two different numbers. Allowed is what Medicare actually allowed in that state, which includes the local practice-cost adjustment. Standardized strips that geographic adjustment out of the payment, so it is the column to use when comparing states — a difference there reflects how the code was billed, not what it costs to run a practice locally.

State	Services	Allowed	Standardized pmt	Providers
Florida	2,327	$341.56	$341.59	3
California	442	$340.26	$341.59	2
Tennessee	191	$341.59	$341.59	2
Arizona	44	$340.92	$341.59	2
Maine	34	$341.59	$341.59	1
Connecticut	28	$341.59	$341.59	1
New Jersey	22	$341.59	$341.59	1
New York	21	$341.59	$341.59	1
Colorado	18	$341.59	$341.59	1
Washington	15	$341.59	$341.59	1
Kentucky	15	$341.59	$341.59	1
Georgia	15	$341.59	$341.59	1
Virginia	13	$341.59	$341.59	1
Illinois	12	$341.59	$341.59	1
Texas	11	$341.59	$341.59	1

Related codes

81339Gene analysis (mpl proto-oncogene$180.81
81307Gene analysis (partner and localizer of brca2) full sequence analysis$661.26
81321Gene analysis (phosphatase and tensin homolog)$586.31
81317Gene analysis (postmeiotic segregation increased 2 [s cerevisiae]) ful$662.97
81325Gene analysis (peripheral myelin protein 22)$753.85
81345Gene analysis (telomerase reverse transcriptase) targeted sequence ana$181.48
81334Gene analysis (runt related transcription factor 1) targeted sequence$322.92
81309Gene analysis (partner and localizer of brca2) targeted sequence analy$269.32
81312Gene analysis (poly[a] binding protein nuclear 1) for abnormal alleles$132.54
81320Gene analysis (phospholipase c gamma 2) for common variants$285.53
81302Gene analysis (methyl cpg binding protein 2) full sequence analysis$516.68
81374Hla class i typing$72.72

Billing this code is not the same as earning it

An allowed amount is revenue to a practice, not income to a clinician. It funds staff, premises, equipment and supplies before anyone is paid. What clinicians actually earn is published separately by the Department of Labor, and what industry pays them is published separately again by CMS — this site carries both.

What doctors are paid →·Look up a clinician →·All procedure codes →

Where this comes from. CMS Medicare Physician & Other Practitioners, by Provider and Service, 2024. It covers fee-for-service Original Medicare Part B only — not Medicare Advantage, not Medicaid, and not commercial insurance, which typically pays more for the same code.

How it is averaged. CMS publishes one average per provider per code. Every figure here is re-weighted by the number of services, so a clinician who billed the code 4,000 times counts 4,000 times more than one who billed it twice. CMS also suppresses any provider-code pair with fewer than 11 beneficiaries, so low-volume practice is missing from these totals by design.