CPT Code 81479: Unlisted Molecular Pathology Procedure

What is the 81479 CPT code all about?

CPT code 814779 is one of the many molecular pathology procedure codes you can use. Each specific molecular pathology CPT code under each group is tied to a specific molecular pathology procedure. Starting January 1, 2013, CPT updates aimed to make coding for molecular pathology services more detailed by focusing on specific analytes and genes. These changes also helped reduce or eliminate the need for “code stacking” when billing. Now, CPT and HCPCS codes cover all the analytical steps involved in the test. As a result, the codes are organized into the following subgroups (Centers for Medicare & Medicaid Services, 2025):

• Genomic sequencing procedures
• Multianalyte assays with algorithmic analyses (MAAAs)
• Proprietary laboratory analyses (PLA codes)
• Tier 1 – Analyte-specific codes where each test or procedure has its own CPT code
• Tier 2 – For molecular pathology services that are low volume or related to rare diseases

Providers should use the procedure code that best matches the service they're performing. If there's no Tier 1 code for the test or the Tier 2 codes don’t quite fit, they should go with the unlisted molecular pathology code, 81479.

Please note that CPT codes under the groups for molecular pathology procedures change every now and then. The official CMS billing and coding article revised and published recently updated back in January 1, 2025, has several changes, so check if your procedure has an assigned CPT code because it's possible that codes have been added. It's just good practice to check for any HCPCS CPT code updates from any resources or references that have a CPT HCPCS codes section.

If your specific procedure isn't on any of the groups, you may use this unlisted molecular pathology CPT code.

CPT code 81479 documentation requirements

Before reporting and billing with this CPT code, please ensure you have the following documentation requirements:

• Please indicate a full description of the molecular pathology procedure you conducted, including your methodology, test targets, and purpose, to argue that it was reasonable and necessary.
• A clinical indication and rationale for selecting the pathology CPT code 81479.
• The date of service and how long the procedure took.
• All relevant laboratory reports with results and interpretations, and if available, proprietary laboratory analyses (PLA).
• Any comparisons to existing codes and justifications for the use of an unlisted procedure.

CPT code 81479 billing guidelines

Besides documentation requirements, it would be best to review the CMS's official article Billing and Coding: Molecular Pathology and Genetic Testing, especially the Group 1 codes. It's good to be up to date with the whole thing and related literature, including CMS IOM publication 100 manuals, Code of Federal Regulations references (specifically CFR Title 42 sections), etc.

Also, you typically wouldn’t bill for more than one separate genetic lab test for the same patient on the same day. But if there’s a rare case where more than one test is truly needed, you’ll need to confirm that each test is a separate service by using the 59 modifier when billing.

Make sure to include the name of the test procedure you conducted (including any electronic or paper claims). These are important. If they're not present, you will be asked to revise and resubmit your claim.

Other CPT codes for molecular pathology services

The following CPT codes also fall under genetic and molecular diagnostic testing:

• 81106 – Human platelet antigen 2 (HPA-2) genotyping, GP1BA (glycoprotein Ib [platelet], alpha polypeptide [GPIbα])
• 81107 – Human platelet antigen 3 (HPA-3) genotyping, ITGA2B (integrin, alpha 2b [platelet glycoprotein IIb of IIb/IIIa complex], antigen CD41 [GPIIb])
• 81108 – Human platelet antigen 4 (HPA-4) genotyping, ITGB3 (integrin, beta 3 [platelet glycoprotein IIIa], antigen CD61 [GPIIIa])
• 81121 – IDH2 (isocitrate dehydrogenase 2 [NADP+], mitochondrial) (e.g., glioma), common variants (e.g., R140W, R172M)
• 81161 – DMD (dystrophin) (e.g., Duchenne/Becker muscular dystrophy) deletion analysis, and duplication analysis, if performed
• 81162 – BRCA1 (BRCA1, DNA repair associated), BRCA2 (BRCA2, DNA repair associated) (e.g., hereditary breast and ovarian cancer) gene analysis; full sequence and duplication/deletion analysis

Reference

Centers for Medicare & Medicaid Services. (2025, January 1). Article - billing and coding: Molecular pathology and genetic testing (A58917). https://www.cms.gov/medicare-coverage-database/view/article.aspx?articleid=58917