CMS's Preliminary 2027 CLFS Rates: Molecular Pathology Tests Take the Deepest Cut
Short answer: CMS released preliminary CY2027 Clinical Laboratory Fee Schedule rates on September 21–22, 2026, showing molecular pathology codes falling a weighted-median 22% and genomic sequencing codes falling 23%, roughly 1.4 times the 16% average cut across all 1,528 priced codes. A statutory 15%-per-year cap will phase in most of that reduction over 2027 and 2028. Final rates publish in November 2026 for a January 1, 2027 effective date, with public comments due by September 21, 2026.
What CMS actually released
The preliminary rates are the output of the second full PAMA private-payor reporting cycle: 6,411 laboratories submitted data on payments received between January 1 and June 30, 2025, up 230% in reporting participation since the first cycle in 2017. Of 1,947 applicable HCPCS codes, 1,528 (78.5%) received a new weighted-median private-payor rate. CMS says 1,171 of those codes are priced lower than their CY2026 rate, 169 are unchanged, and 186 increased. Across the priced code set, CMS estimates the average reduction at roughly 16% and projects about $1 billion in annual Medicare Part B savings once fully phased in.
This is the mechanical follow-through on the PAMA market-based rate-setting law that molecular labs have been anticipating since the 15%-per-year reduction cap resumed after six years frozen at 0%, a shift we covered when CMS opened the reporting cycle. What's new this month is the actual data: category-level percentage cuts and code-level dollar figures labs can now use to model 2027 revenue, rather than the general mechanism.
Molecular and genomic codes are absorbing the deepest cuts
The category breakdown is the headline for molecular labs specifically. Proprietary Lab Analysis (PLA) codes — the single-source, often exclusive-license codes many precision-diagnostics companies rely on — saw the smallest average reduction, just 2.4%. Chemistry fell 16%, in line with the overall average. Microbiology and immunology codes fell 19.3%. But molecular pathology fell 22%, and genomic sequencing procedures fell 23%, making them the two hardest-hit categories in the entire CLFS.
The likely driver is that PAMA's private-payor benchmark reflects rates commercial insurers negotiated during a period when payers were aggressively renegotiating molecular and genomic test contracts, while PLA codes' single-source pricing gave payers less room to negotiate down. For labs that built 2027 budgets around the generic "up to 15% a year" framing, a 22–23% category average is a materially different planning number.
The category average hides enormous code-by-code swings
Averages flatten a much messier reality underneath. CMS's full rate file — roughly 100 megabytes across seven worksheets, per analysis from Discoveries in Health Policy — shows individual PLA and molecular codes moving far outside the category trend in both directions. A 51-plus-gene tumor panel (CPT 81455) barely moved, down about 2%, from $2,919 to $2,861. Illumina's TruSight Oncology assay (0543U) fell 55%, from $2,989 to $1,337. Adaptive Biotechnologies' clonoSEQ MRD assay (0364U) dropped 83%, from $2,007 to $337. A thrombocytopenia genetic panel (0276U) fell 98%, from $2,448 to just $45.
Other codes moved sharply higher: Caris Life Sciences' liquid-biopsy assay (0485U) rose 44% to $5,250; Silbiotech's BBDRisk Dx (0067U) rose 76% to $3,330; Grifols' BLOODchip ID (0084U) more than tripled, up 206% to $2,205; and one Mayo Clinic monitoring test (0382U) jumped from $51 to $962, an increase of more than 1,700%. Caris' MI Cancer Seek (0211U) remained the highest-priced code in the file, unchanged at $8,455.
These outliers are a known artifact of PAMA's methodology for low-volume, single-source PLA codes: a small change in which payers report data, or how many claims they report, can swing a weighted median dramatically year to year. Labs billing any of these specific codes should pull their own CY2027 preliminary rate from the CMS file rather than assuming the category average applies.
The 15% cap softens the landing — but not for as long as you might think
PAMA law caps any single code's year-over-year reduction at 15%, with that cap running through 2027, 2028, and 2029. It's tempting to assume a large cut like molecular pathology's 22% average gets smoothed evenly across all three years. It doesn't. The cap only applies until a code reaches its actual market-based target rate — after that, the reduction stops, regardless of how many years remain in the statutory window.
Run the math on a representative $1,000 molecular pathology test facing the category's 22% target reduction: the 15% cap takes it to $850 in 2027. Only about 8.2 percentage points of cut remain to reach the $780 target, well under the 15% cap, so that remainder lands entirely in 2028. The code is at its full, market-based rate by January 1, 2028 — a year earlier than the three-year cap window might suggest. The same arithmetic applies to genomic sequencing's 23% target. Codes facing steeper cuts than roughly 28% in a single cycle are the ones that will actually stretch into a third year.
CAP is calling the cuts unsustainable — and pushing Congress for a fix
The College of American Pathologists responded to the preliminary rates by renewing its push for the RESULTS Act, federal legislation that would overhaul how CMS sets CLFS rates under PAMA. CAP leadership has characterized the current market-based methodology as unsustainable at this scale, arguing it threatens laboratory infrastructure, particularly for hospital and health-system labs that have grown fastest under PAMA (hospital lab reporting entities are up more than 4,000% since 2017) but tend to have thinner margins on molecular volume than large reference labs. The American Clinical Laboratory Association and other lab trade groups have raised similar concerns in comments on the broader CY2027 rulemaking, including a separate, unrelated CMS proposal to move certain software-driven laboratory analyses onto the hospital outpatient fee schedule instead of the CLFS.
None of this changes the November timeline. Public comments on the preliminary rates were due September 21, 2026; CMS is not obligated to change the methodology in response, only to consider input before finalizing.
What labs, RCM teams, and ordering clinicians should do now
Molecular labs and RCM teams have roughly six weeks between the preliminary rate release and CMS's November final publication. That window is for modeling, not lobbying:
Pull your own code-level preliminary rates
Don't budget off the 16% or 22% category averages. Download CMS's preliminary CY2027 rate file and check every CPT/PLA code your lab actually bills — the swings above show category averages can misrepresent a specific code by 50 percentage points or more in either direction.
Model 2027 revenue under the two-year-to-target scenario, not a flat 15%/year assumption
For most molecular and genomic codes, the full cut lands by 2028. Build cash-flow projections that reflect a bigger 2027 hit followed by a smaller 2028 adjustment, rather than assuming three equal annual reductions.
Flag high-volume PLA codes for extra scrutiny
Because PLA rate swings are driven by thin, single-source reporting samples, a lab's most-billed proprietary code deserves individual verification against the CMS file, not an assumption that "PLA codes only fell 2.4% on average."
Watch for the final rule in November
Preliminary rates can and do shift before finalization. Set a calendar reminder to re-check final CY2027 rates against your preliminary-rate model as soon as CMS publishes them, and before locking 2027 payer contracts or budgets that reference Medicare CLFS as a benchmark.
Frequently asked questions
When do the new CY2027 CLFS rates take effect?
The rates released in September 2026 are preliminary. CMS will publish final CY2027 rates in November 2026, and they take effect January 1, 2027, alongside the resumption of PAMA's 15%-per-year reduction cap after six years at 0%.
Are the September 2026 rates final, or could they still change?
They're preliminary. CMS accepted public comments through September 21, 2026, and can revise rates before the November final publication. Labs should treat the September figures as a strong planning signal, not a locked number.
Why were molecular pathology and genomic sequencing cut more than other categories?
Both categories fell further than the roughly 16% overall average — 22% and 23% respectively — based on the weighted median of what commercial payers actually paid for those codes between January and June 2025. CMS has not published a category-specific explanation beyond the private-payor data itself.
Does the 15% annual cap mean my molecular test rate won't fully drop until 2029?
Not necessarily. The cap limits any single year's cut to 15%, but stops once a code reaches its market-based target. For the ~22% molecular pathology average, that means roughly 15% in 2027 and the remaining 8% in 2028 — full effect by 2028, not 2029.
What should labs do differently in the six weeks before November's final rates?
Pull code-level (not category-average) preliminary rates for everything your lab bills, model 2027 cash flow around the two-year phase-in math above, and flag any high-volume PLA codes for individual verification given how volatile those specific rates can be.
This article is intended for laboratory, revenue-cycle, and clinical-operations professionals evaluating Medicare payment policy and does not constitute billing, coding, legal, or medical advice. Coverage and payment determinations should always be verified against the current CMS Clinical Laboratory Fee Schedule file and applicable Medicare Administrative Contractor guidance.
Sources: CMS, "Preliminary Calendar Year (CY) 2027 Medicare Clinical Laboratory Fee Schedule Payment Rates" fact sheet (September 2026); CLP Magazine, "CMS Releases Preliminary 2027 CLFS Rates as CAP Calls for Payment Reform" (September 22, 2026); Discoveries in Health Policy, "CMS Posts 'PAMA' Lab Fee Schedule for 2027 Forward" (September 21, 2026); ScreenMyGene, "PAMA-Based Rate Cuts Resume on the 2027 CLFS" and "The 2027 PLA Code Application Deadline". For background on how Medicare covers molecular and genetic testing more broadly, see the ScreenMyGene resource library.