Billing for molecular (PCR) testing has become a critical area of focus for clinical laboratories, especially as the Centers for Medicare & Medicaid Services (CMS), Medicare Administrative Contractors (MACs), and the American Medical Association (AMA) offer overlapping — but sometimes conflicting — rules.
Understanding the nuances of multiplex PCR billing under CMS/NCCI and AMA guidance is essential for compliance and financial stability.
CMS/NCCI Multiplex PCR Billing Guidelines
One unit of service for panel tests
The CMS National Correct Coding Initiative (NCCI) takes a bundled approach to billing multiplex PCR tests. According to Chapter 10 of the NCCI Policy Manual:
- If a single method or kit detects multiple organisms, laboratories should report one unit of service (UOS).
- For example, a multiplex assay that identifies multiple infectious agents would be billed using CPT 87801.
Novitas guidance and current enforcement
Recently, Novitas, a MAC, reiterated this policy in a 2023 educational article. However, there is currently no local coverage determination (LCD) in place to enforce denials for claims that deviate from this standard — at least not yet.
AMA CPT Coding Rules for PCR Testing
Coding to the highest level of specificity
The AMA CPT coding rules lean in a different direction. Their guidance emphasizes specificity:
- If analyte-specific CPT codes exist (such as CPT 87491 for chlamydia or CPT 87591 for gonorrhea), laboratories should use those codes instead of a generic panel code.
When to use analyte-specific codes
This only applies if results differentiate between organisms. If the assay does not provide organism-level results, the broader CPT 87801 panel code remains correct. In short, the AMA encourages granular billing where possible.
Conflict Between CMS and AMA on PCR Billing
Simplicity vs specificity in reimbursement
The conflict lies in the philosophy of billing:
- CMS/NCCI: Panel code = simpler, cheaper for payers.
- AMA: Separate analyte-specific codes = more precise, authoritative coding.
How enforcement varies across MACs
Both interpretations exist in practice, but enforcement varies across regions and contractors.
Best Practices for Laboratory Billing Compliance
Current risk of denials with multiplex panels
For laboratories, the current environment creates both flexibility and risk. Since Novitas has not yet issued an LCD enforcing strict NCCI edits, claims are not being denied based on panel billing. However, if Novitas or other MACs begins enforcing MUE edits, labs could face sudden denials for incorrectly billed claims.
Aligning with AMA coding for long-term protection
The safest approach is to follow AMA’s specificity-first guidance whenever possible. Use analyte-specific CPT codes when organism-level results are available, and default to the panel code only if the assay does not differentiate results. This strategy aligns with coding authorities and positions laboratories for compliance, even if contractors tighten enforcement later.
Key Takeaways for Multiplex PCR Billing
- CMS/NCCI recommends one unit of service for multiplex panels.
- AMA guidance emphasizes analyte-specific CPT coding where results are distinct.
- Novitas has not yet enforced strict denials, but risk remains.
- More payers are starting to adopt this policy of one-panel coding.
- Laboratories should research and understand payer policies and coding requirements, especially since policies are constantly changing.