Pathology CPT Codes List + Modifiers 2025

Last Updated on September 18, 2025

Pathology CPT coding turns specimens into precise, payable work. The right code tells payers what was examined, how complex it was, and which components (professional vs technical) were performed. 

Below is a practical, search-optimized walkthrough of the must-know Pathology CPT codes, with documentation cues, modifier rules, and 2025 context so new and experienced coders can move quickly and accurately.

Surgical Pathology CPT Codes 88300–88309 (Specimen-to-Level Mapping)

Surgical (anatomic) pathology levels drive a large share of AP revenue. Levels are chosen by specimen complexity, not by the number of blocks or slides. Getting the level right, especially for 88305, the workhorse, keeps claims clean and denials low. Authoritative references still map common specimens to levels (e.g., skin/GI biopsies → 88305; complex resections → higher levels). 

• 88300 – Gross exam only (identification/description; no microscopy).
• 88302–88309 – Gross + microscopic, increasing by specimen complexity; 88305 captures many routine biopsies (skin, GI, cervix, etc.).
• Documentation tip: Name the specimen precisely (“colon, biopsy” vs. “biopsy”). Align with your MAC or institutional specimen-to-level tables to support the selected code.

Intraoperative Consultation & Frozen Section 88329, 88331–88334

Intraop consults must mirror exactly what occurred in the OR, gross consult only, frozen section(s), cytologic touch preps, or a combination. Accurate block/site counts and method drive correct coding and payment.

• 88329 – Intraoperative gross examination (no frozen section).
• 88331 – First tissue block with frozen section(s); 88332 – each additional block.
• 88333 – First cytologic evaluation (e.g., touch imprint) during intraop consult; 88334 – each additional site.
• Documentation tip: Note the surgeon request, specimen/site, number of frozen blocks, and whether cytologic prep was used to support add-on use. (Follow NCCI edits to avoid unbundling).

Special Stains, IHC, IF, ISH, EM

Enhanced studies increase diagnostic accuracy and reimbursement, but unit-of-service and “per specimen” rules matter.

Special Stains 88312–88319 (Microorganisms & Histochemistry)

Use when medically necessary (e.g., GMS for fungi, AFB for mycobacteria). Note the organism/target and rationale in the report; follow payer/medical policy for indications.

Immunohistochemistry (IHC) 88341, 88342, 88344

Report per specimen, tracking single-antibody vs. multiplex use in the note:

• 88342 – Initial single antibody stain (per specimen)
• 88341 – Each additional single antibody stain (same specimen)
• 88344 – Multiplex antibody stain (per specimen)
• Coding tip: Keep an antibody list and medical necessity statement; payers/UM vendors reference these codes directly.

Immunofluorescence (IF) 88346, 88350

Common in dermatopathology and renal biopsies. 88346 covers the initial single-antibody IF stain; 88350 covers each additional antibody on the same specimen (check payer rules). (Maintain antibody/target documentation for appeals.)

In-Situ Hybridization (ISH) 88365–88377

Specify probe(s), target (DNA/RNA), and result interpretation; link to diagnosis rationale in the report to support medical necessity. (Many payer articles cite these codes for oncologic and infectious targets.)

Electron Microscopy 88348

Still indicated for selected renal, neuromuscular, and tumor workups. Ensure the report explains why EM was required for diagnosis. (Avoid legacy/deleted EM codes in templates.)

Cytopathology & Pap Smear CPT Codes

Pap and cytology coding trips up many teams because lab interpretation codes are not collection codes. Pathology bills the cytopathology interpretation; a different HCPCS/CPT may apply to the collection at the clinic. A widely cited AAFP explainer warns that coders often pick 88141–88175 when they actually need the collection code (e.g., Q0091 for Medicare).

• 88142/88175 – Cervical/vaginal cytology (conventional vs. automated/thin-prep with manual rescreen).
• Policy & frequency: Use CMS MLN to verify preventive screening coverage intervals and documentation; match the correct screening vs. diagnostic pathway.

Non-GYN Cytology & FNA Cytopathology

Non-GYN sources (pleural fluid, urine, etc.) require clear source and prep documentation (smear, concentration, cell block). For FNA, coders must separate immediate adequacy from final interpretation:

• 88172 – Immediate adequacy evaluation (e.g., ROSE), typically billed per site/episode.
• 88173 – Final cytopathology interpretation and report (per specimen).
• Coding tip: Many lab/health-system references teach that 88172 may be reported in addition to the aspiration procedure code (e.g., 10021) when performed and documented; follow local payer policy and capture the site count correctly.

Flow Cytometry CPT Codes

Flow is essential in leukemia/lymphoma workups. Separate technical marker counts from professional interpretation, and watch payer caps and “do-not-pair” rules.

• 88184 – First marker (technical)
• 88185 – Each additional marker (technical)
• 88187 / 88188 / 88189 – Professional interpretation (2–8, 9–15, 16+ markers)

Coverage cautions: Medicare articles and payer policies prohibit combining 88184–88185 with certain 86355–86367 quantitative codes for the same analysis, and clarify how/when 88187–88189 are used. Always check NCCI edits and local coverage before billing.

Molecular Pathology & NGS Panels 

Precision oncology depends on correct selection of Tier 1 single-gene codes vs. NGS panel codes. Align orders with coverage policies and document tumor type, panel size, and clinical rationale.

• Common Tier 1 examples: 81235 (EGFR), 81210 (BRAF), 81275 (+81276) (KRAS).
• Oncology panels: 81445 (solid organ tumor panel, 5–50 genes), 81450/81455 (hematolymphoid 5–50 / expanded 51+).
• Coding tip: Use payer articles to decide when a panel (81445) is appropriate versus stacking single-gene codes; build reflex pathways in the LIS to keep orders, documentation, and claims consistent.
  

Outside Pathology Consultations

Second-opinion consultations arrive as “cases,” often with slides prepared elsewhere. Bill per case at the appropriate intensity and avoid double-billing stains performed by the originating lab.

• 88321 – Slide review/consultation on outside prepared slides (with report).
• 88323 – Consultation with slide preparation from referred blocks.
• 88325 – Comprehensive consultation, including review of records/specimens and report.
• Documentation tip: State that slides were prepared elsewhere and describe the scope of review; add-on stains performed by your lab can be billed when you perform them. (Follow MAC guidance for units/coverage.)

Pathology Modifiers

Split-billing (Professional vs. Technical):

• -26 (Professional component) – Pathologist’s interpretation only.
• -TC (Technical component) – Facility/lab work (equipment, supplies, staff).
  Know who bills which component (hospital vs. path group), and match your claim form to payer PC/TC rules to prevent payment splits or takebacks. (Consult payer modifier pages and PC/TC indicators.)
• -90 – Append when your entity bills for a test performed by another lab (some payers restrict for AP; check MAC policy and claim form requirements like CLIA, performing lab address). (This is a common AR delay when left off.)

• -91 – Repeat clinical diagnostic lab test (same day, medically necessary), do not use for QC repeats.
• -59 – Distinct procedural service (use sparingly; prefer specific modifiers when available).
• -92 – Alternative lab platform testing (e.g., single-use cartridge/kit platforms when CPT allows).

2025 Pathology/Lab CPT Changes

For 2025, Pathology/Lab saw 114 additions, 14 deletions, and 9 revisions. That level of change affects fee schedules, coverage, and charge masters, especially in molecular and digital workflows. Leadership should post a changelog, retrain coding teams quarterly, and update EMR/LIS picklists to match current CPT and payer policy. Scope reminder: Path/Lab CPT spans 80047–89398 across organ-disease panels, chemistry, microbiology, transfusion, surgical pathology, cytology, and more,so index pages and training decks should reference the full family.