Key Takeaways
- Medicare Administrative Contractors are denying claims that bill one unit of CPT 87798 for each organism detected by a single multiplex infectious disease panel.
- The National Correct Coding Initiative (NCCI) Policy Manual, Chapter 10, says a test for multiple infectious agents is reported with one unit when one procedure, one methodology, or one test kit is used, citing 87800 and 87801 as examples.
- AMA CPT guidelines say separately reported results for different organisms should each be coded, which many labs read as support for multiple units of 87798.
- Transitioning unspecified organism testing from multiple units of CPT 87798 to one unit of CPT 87801 may reduce Medicare reimbursement for a six-organism panel by about two-thirds.
- Respiratory, gastrointestinal, and central nervous system panels have their own CPT codes and should be billed under those codes.
Nearly every molecular laboratory we work with is dealing with Medicare denials on CPT 87798 this year. The claims share a pattern: a lab runs one multiplex panel on one patient sample, bills a unit of 87798 for each unspecified organism the panel tests for, and the Medicare Administrative Contractor (MAC) partially denies the claim. This post explains the coding conflict behind those denials, how to choose the right code for a multiplex panel, and what labs can do to protect revenue and compliance.
Why are MACs denying multiple units of CPT 87798?
MACs are denying multiple units of 87798 because NCCI policy treats a single multiplex test run as one service, regardless of how many organisms it detects. When one procedure, one methodology, or one test kit produces results for several organisms, Medicare expects one unit of a multiple-organism code such as 87801. NCCI edits are a common source of coding-related denials.
NCCI’s one-unit rule predates 2026, and MACs have tightened enforcement this year. On July 15, 2026, First Coast Service Options published Bill infectious disease panels correctly, naming multiple codes billed for a single test kit as the first of three common errors on infectious disease panel claims. Novitas Solutions has published guidance under the same title. Across the molecular labs we work with, we’re seeing denials from multiple MAC jurisdictions.
What is the difference between CPT 87798 and CPT 87801?
CPT 87798 reports detection of one infectious organism that has no organism-specific code, billed once per organism. CPT 87801 reports detection of multiple organisms in a single test, billed as one unit for the panel. Both use amplified probe technology such as PCR.
| CPT 87798 | CPT 87801 | |
| Descriptor | Infectious agent detection by nucleic acid (DNA or RNA), not otherwise specified; amplified probe technique, each organism | Infectious agent detection by nucleic acid (DNA or RNA), multiple organisms; amplified probe(s) technique |
| Intended use | One organism with no organism-specific CPT code | Multiple organisms detected in a single test |
| Units under NCCI | One per organism, when separate procedures are performed | One per procedure, methodology, or test kit |
| Approximate 2026 Medicare rate | About $35.09 per unit | About $70.20 per test |
Under NCCI, the code and unit count follow how the test is performed. One panel run on one platform in one pass is reported as one unit of 87801, whether it screens for three organisms or 15.
What does NCCI Chapter 10 say about multiplex infectious disease panels?
The NCCI Policy Manual for Medicare, Chapter 10, covers pathology and laboratory services (CPT codes 80000-89999). Section M.15 addresses unit reporting for infectious agent testing:
“CPT codes that test for multiple infectious agents are reported with one unit of service if one procedure, one methodology, or one test kit is used to perform the test (e.g., 87300, 87451, 87800, 87801).”
The same section allows more than one unit when the testing calls for it: “When multiple procedures, multiple methodologies, or multiple kits are medically necessary and used to perform a test for multiple infectious agents, the units of service reported for CPT codes that identify multiple infectious agents equals the number of different procedures, methodologies, or kits used.”
Section K.5 requires aggregation of applicable targets for the specified multiplex code families when additional testing uses the described molecular methodologies within the scope of the panel. Medically reasonable and necessary testing using a different methodology, or for other microorganism types not included in the multiplex test, may be separately reportable, subject to applicable coding and coverage requirements.
Why do AMA and NCCI guidance conflict on 87798?
AMA CPT guidance and NCCI policy start from different principles. The CPT microbiology guidelines, as published in an AMA CPT Assistant special edition, state: “When separate results are reported for different species or strain of organisms, each result should be coded separately.” Modifiers 59 or XU apply when separate results are reported for different species or strains that are represented by the same CPT code. The same guidelines advise that 87798 should be selected for organisms that have no specific CPT code. Additionally, the AMA publication states that “even if a laboratory procedure produces multiple reportable test results, only a single CPT code may be reported for the procedure,” which aligns more closely with the NCCI position on reporting these services.
Many laboratories have interpreted this guidance as supporting evidence for reporting multiple units of CPT 87798 when a panel generates distinct results for organisms that do not have their own organism-specific codes. In contrast, NCCI considers a single multiplex assay run to be reportable as only one unit of service. Historically, Medicare contractors did not consistently enforce the NCCI interpretation, which contributed to the widespread industry practice of billing per organism. We discuss the history and implications of this discrepancy in our article, “Navigating PCR Billing: CMS vs AMA Guidance on Multiplex Testing.” For Medicare claims, however, current MAC enforcement aligns with the NCCI position.
When should a multiplex panel use a panel-specific CPT code?
A multiplex panel should use a panel-specific CPT code whenever one describes the test. Several common syndromic panels have their own codes:
- Respiratory pathogen panels: 87631-87633, plus 87636-87637 for combined SARS-CoV-2 and influenza testing
- Gastrointestinal pathogen panels: 87505-87507
- Central nervous system pathogen panels: 87483
MACs also apply coverage policies to these panels. First Coast’s July 2026 article points to its local coverage determinations for respiratory panel testing (L38918) and gastrointestinal pathogen panels (L38227), the latter allowing only one GI multiplex panel per day per beneficiary. 87798 and 87801 apply only to organisms and combinations without a more specific code.
For MACs participating in the MolDX Program (Palmetto GBA, Noridian, WPS, and CGS), billing is subject to more stringent coverage and coding requirements. Under these guidelines, CPT 87801 requires an approved DEX Z-Code to identify the specific molecular diagnostic test being performed. Palmetto GBA outlines these requirements in LCD L38988 and the associated billing and coding article A58710, and the other MolDX contractors publish parallel documents under their own numbers. Labs should review them to ensure compliance with MolDX billing policies.
How much revenue is at stake when 87798 is transitioned to 87801?
For panels that detect four or more organisms and include a combination of organism-specific CPT codes and 87798, transitioning from reporting multiple individual CPT codes (often referred to as a coding stack) to a single unit of CPT 87801 can reduce Medicare reimbursement by about half or more. Under the 2026 Clinical Laboratory Fee Schedule, CPT 87798 reimburses approximately $35.09 per unit, while CPT 87801 reimburses approximately $70.20 per test. As an example, a six-organism PCR panel billed as a coding stack, where most codes reimburse about $35.09, may reimburse approximately $210. When the same panel is reported as a single unit of 87801, reimbursement drops to approximately $70. Rates vary by code and test type, so the difference will be different for other panel types, such as hematology panels.
These totals do not include the additional 2% Medicare sequestration reduction, which is applied to the final payment amount.
The reduction applies to tests the lab has already run and paid to process. For labs with large PCR volumes, the loss adds up across a month of claims. Lab reimbursement faces separate pressure from the preliminary 2027 CLFS rates, which would cut Medicare payment for 1,171 lab codes.
What should labs do to reduce 87798 denials?
Labs can reduce 87798 denials by aligning unit counts with how each test is performed and documenting that methodology. Priorities:
- Match the code to the test run. If one kit, one methodology, and one procedure produced the results, report one unit of 87801 (or 87800 for direct probe testing), regardless of how many organisms the panel covers.
- Check for a panel-specific code first. Respiratory, GI, and CNS panels have dedicated codes and coverage policies.
- Document the methodology along with the results. Records should show how many distinct procedures, methodologies, or kits were used, since that determines the unit count under NCCI.
- Review medically unlikely edit (MUE) limits. Check the current CMS MUE tables for 87798 and other codes your lab bills in multiple units, since units above an MUE are denied.
- Screen claims before submission. A medical claim scrubber can flag NCCI bundling conflicts, such as a panel code billed alongside its component tests.
- Audit recent claims. Review 87798 claims billed in multiple units before a MAC requests records or places claims on prepayment review. Laboratory analytics can show denial trends by code and payer.
- Prepare appeal documentation in advance. Where multiple units reflect separate testing, have the supporting records ready before billing.
When can a lab still bill multiple units of 87798?
A lab can bill multiple units of 87798 when it performs separate, medically necessary procedures to detect different organisms that have no organism-specific CPT code. NCCI Chapter 10 ties the unit count to the number of distinct procedures, methodologies, or kits used. Two separate assays run on different platforms for two unlisted organisms, for example, can support two units. A single multiplex run supports one unit, even if it reports each organism separately.
How PGM Helps Molecular Labs Bill Multiplex Panels Correctly
PGM’s lab billing team helps laboratory clients navigate and address the coding, documentation, and payer policy challenges associated with 87798 denials, including compliance with MAC-specific billing requirements. Labs seeking an evaluation of their PCR billing can contact PGM’s laboratory billing and RCM team through our contact page to discuss coding strategies, reimbursement considerations, and payer-specific requirements.
* * *
Frequently Asked Questions About CPT 87798 and 87801
Can modifier 59 be used to bill multiple units of 87798 for one panel?
Not to split a single panel into components. CPT guidelines call for modifier 59 when separate results for different species or strains are described by the same code, but the NCCI Policy Manual, Chapter 1, says modifiers should not be used solely to bypass an NCCI edit. First Coast lists improper modifier use as one of the three most common errors on infectious disease panel claims. Modifier 59 is also subject to heightened scrutiny by CMS and other payers and is frequently cited as an audit trigger, so its use should be supported by clear documentation that the services were distinct and separately reportable.
Is the one-unit rule for multiplex panels new?
No. NCCI has long instructed labs to report one unit for a multiple-organism test performed with one procedure, methodology, or kit, and several non-MolDX MACs had published guidance on billing infectious disease panels well before 2026. The change in 2026 is how consistently MACs are enforcing it.
Does correct coding guarantee Medicare coverage?
No, correct coding and medical necessity are separate Medicare requirements, and a claim must satisfy both criteria for payment. A lab may report the appropriate panel CPT code with the correct number of units and still receive a denial if medical necessity is not supported. To meet medical necessity requirements, the patient’s medical record must demonstrate that the test was clinically indicated, justify why a broad multi-pathogen panel was necessary instead of more targeted testing, and show how the results reasonably impact patient management or treatment decisions. Documentation must also support that the test was performed within its validated patient population and specimen type. In addition, many LCDs impose panel-specific requirements such as limitations on repeat testing, frequency restrictions, or additional documentation standards. Failure to meet these coverage criteria may result in denial, even when the claim is coded correctly.
How do MolDX contractors handle multiplex infectious disease panels?
MolDX contractors treat each syndromic panel as a single unit of service. Palmetto GBA’s billing article A58710 states that a panel “is characterized by a single unit of service (UOS =1)” and cannot be unbundled into individual components, even when it reports multiple pathogens. Panels without their own CPT or PLA code are billed with unlisted code 87999.
Do commercial payers follow the NCCI one-unit rule?
Many commercial payers either adopt NCCI edits or publish their own laboratory coding and reimbursement policies, which means the single-unit reporting requirement may apply to commercial claims as well as Medicare claims. Payers like UHC and Humana have enforced these guidelines. Labs should review the laboratory reimbursement and multiplex testing policies of each major payer to ensure compliance with payer-specific billing requirements and avoid denials or audit risks.