Special Stains

April 16, 2021

APS performs regular audits of client report documentation, CPT®/ICD-10 code assignment and their possible relation to carrier edits. One area that APS auditors see as problematic, is proper CPT code assignment for special stains. Following is a breakdown of this area. 

Histologic special stains, including histochemistry and cytochemistry stains, are reported with CPT codes in the range 88312-88319.

  • 88312 - Special stain including interpretation and report; Group I for microorganisms (e.g., acid fast, methenamine silver)
  • 88313 - Special stain including interpretation and report; Group II, all other (e.g., iron, trichrome), except stain for microorganisms, stains for enzyme constituents, or immunocytochemistry and immunohistochemistry
  • 88314 - Special stain including interpretation and report; histochemical stain on frozen tissue block (List separately in addition to code for primary procedure)
  • 88319 - Special stain including interpretation and report; Group III, for enzyme constituents

The unit of service for CPT codes 88312, 88313 and 88319 is one unit for each special stain, on each surgical pathology block, cytologic specimen or hematologic smear. Report one unit of 88314 for each special stain on each frozen section block. Both the AMA and Medicare are in agreement with the definition of the unit of service for special stain codes 88312-88319 as of January 1, 2012. As stated, codes 88312, 88313, 88319 are reported per block. To clarify; a single block includes all multiple levels cut from the same block of tissue stained with the same stain.

Per CPT, code 88312 or Group I is assigned to a special stain when looking for microorganisms. The term microorganism in this context is unrestricted by class of organism (e.g., bacteria, fungi, parasites, protozoa). Although a Group I stain can arise with many different tissues, most often they are performed on gastric, esophageal, and lung biopsies, looking for helicobacter pylori (giemsa); fungi (PAS); and fungi, acid fast bacilli, or gram positive organisms.

Code 88313 or Group II would be assigned when used to highlight substances such as glycogen, collagen, mucin, iron, reticulin, copper and zinc in tissue specimens, but it doesn’t cover enzymes which is code 88319, and it’s not to be confused with immunoperoxidase (88342) or immunofluorescence (88346-88350).

Further, if a special stain usually reported with 88313 is applied to snap frozen tissue instead of paraffin fixed tissue, report 88314 instead of 88313.

Documentation will need to support each block. Acceptable documentation would be the name of each different stain used per block/per specimen and results. Logs, worksheets, and order slips, whether electronic or hardcopy, typically don’t constitute acceptable medical documentation for charge support purposes; so a special stain supported by an order slip or worksheet entry, but not mentioned anywhere in the formal pathology report, should not be charged.

It’s not necessary that you stipulate what you found when you looked at a stain, so provide that information only to the extent it’s meaningful for medical communication. Dedicate a special area on the report to document special stains, such as the final diagnosis, or a comment section, under a “Special Procedure” section or if you document a micro exam consistently, it could be in that section.

1)    The AFB and GMS stains are performed on both blocks A1 and A2 are negative for acid fast bacilli and H-pylori. 
Code 88312 x 4
2)    Stains performed on a liver biopsy. Iron stain is negative, trichrome shows a normal amount of collagen within portal tracts, reticulin stain shows a normal reticulin pattern, PAS and PAS-D negative.
Code 88313 x 5

All codes in the 88312-88319 range have both a professional and a technical component, so modifiers -26 and TC need to be added appropriately.

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Special Stains (575.67 KB)