Identify How to Get Paid for Special Stains

Identify How to Get Paid for Special Stains

Payers are looking for more than just the correct codes for non-routine pathology stains.

Pathology stains are crucial for the diagnostic evaluation of tissue samples by pathologists. There are many types of stains, which are categorized as either routine hematoxylin and eosin (H&E) stains or special stains. This article explains some of the different types of special stains, how to code them, and documentation requirements for these non-routine pathology orders.

Coding Special Stains

Stains identify important tissue features and enhance tissue contrast, which pathologists use to provide a complete and accurate tumor diagnosis. Examination of tissues has its own branch of study called histology. Histology is a branch of anatomy that makes up the minute structures of animal and plant tissues that are only discernible under a microscope.

Coding for pathology services is based on the source of the tissue being examined. H&E stains are standard stains used by all pathology laboratories for microscopic examination of tissue and are included in the base pathology CPT® code range 88301-88309. These routine stains enhance tissue morphology: hematoxylin stains a cell’s nucleus a bluish color and eosin stains a cell’s nucleus pink (Figure 1).

Special stains are sometimes necessary to discern minute structures, inclusions, antigens, and chemical constituents. According to the Department of Justice, “The government considers the use of special stains before the analysis of the routine H&E stained specimen to be medically unnecessary.”

The Centers for Medicare & Medicaid Services (CMS) requires documentation for special stains include not only the stain results but also why the additional testing was done. Only a pathologist may determine the medical necessity of a special stain, but Local Coverage Decision (LCD) L36351 states, “… it is the obligation of each entity to independently assure the medical necessity of the services renders by each entity.” Linking the stain to its purpose is essential to avoid claim denials.

Group I Special Stains: CPT® 88312

CPT® code 88312 Special stain including interpretation and report; Group I for microorganisms (eg, acid fast, methenamine silver) is not specific to any category of microorganism but is used to observe bacteria, fungi, parasites, yeast, and protozoa. Examples of Group I stains and their purpose include, but are not limited to:

1. Acid Fast stain – Mycobacterium tuberculosis (Figure 2).

2. Steiner stain – Used to identify fungi, Helicobacter pylori, legionella pneumophila (Figure 3), and spirochetes.

3. Grocott methenamine silver (GMS) stain – Used to identify fungi, this stain colors fungi black on a green background (Figure 4).

Group II Special Stains: CPT® 88313

CPT® code 88313 Special stain including interpretation and report; Group II, all other (eg, iron, trichrome), except stain for microorganisms, stains for enzyme constituents, or immunocytochemistry and immunohistochemistry is used for cellular components such as iron, reticulin, collagen, and zinc. Examples of Group II stains and their purpose include, but are not limited to:

1. Alcian Blue stain – Reliable stain used for the identification of acidic polysaccharides such as goblet cells seen in Barrett’s esophagus (Figure 5).

2. Gomori Prussian Blue Iron stain – Used to detect loosely bound iron in tissue sections, bone marrow smears, and blood smears (Figure 6). Increased amounts of iron may be an indicator of hemochromatosis or hemosiderosis.

Trichrome – Used to visualize collagen in tissue sections. Collagen is stained blue, nuclei are stained dark brown, muscle tissue is stained red, and cytoplasm is stained pink. Trichrome staining is used in the diagnosis of muscular dystrophy, cirrhosis, glomerular fibrosis, liver and kidney tumors, and more.

Group III Special Stains: CPT® 88319

CPT® code 88319 Special stain including interpretation and report; Group III, for enzyme constituents is used for enzymes such as esterase, myeloperoxidase, and phosphatase. Examples of Group III stains and their purpose include, but are not limited to:

1. Myeloperoxidase stain – A method used to determine lineage per World Health Organization classification for acute myelogenous leukemia from acute lymphoblastic leukemia (Figure 7).

2. Sudan Black stain – Used for identifying lipids such as phospholipids, sterols, and triglycerides (Figure 8). Lipids and fat stain blue-black and cell nuclei stain red.

3. ATPase stain – Used to distinguish muscle fiber types at different pH levels (Figure 9).

Immunohistochemical Stains: CPT® 88342

CPT® code 88342 Immunohistochemistry or immunocytochemistry, per specimen; initial single antibody stain procedure is used for identifying substances and cells in tissue sections, while add-on CPT® code 88341 Immunohistochemistry or immunocytochemistry, per specimen; each additional single antibody stain procedure (List separately in addition to code for primary procedure) is used for each additional single antibody stain procedure.

The antigen-antibody reaction is at the heart of these stains. Antibodies to more than 400 distinct targets are available. Examples of immunohistochemical stains include, but are not limited to:

  • Her2 – Important in determining the Her2 status in breast cancer.
  • Kappa-Lambda – Kappa and Lambda antibodies aid in the diagnosis of myelomas, plasmacytomas, and certain non-Hodgkin’s lymphomas.
  • Inhibin – A hormone produced by ovarian and testicular cells. Inhibin staining aids in the diagnosis of sex cord-stromal tumors.

Under the Microscope

Understanding how special stains are used by pathologists to aid in the identification and diagnosis of medical conditions and how they differ from H&E stains are key to proper coding. Remember, however, that evidence of medical necessity is paramount and it’s the responsibility of everyone involved in the medical claim to ensure the criteria for use of special stains are met.


CMS L36351 Lab: Special Histochemical Stains and Immunohistochemical Stains (effective 10/15/2015).

DOJ. Hickory Pathology Lab Agrees to Pay the United States $301,000 to Settle False Claims Act Allegation. May 2, 2017.

Frank Mesaros
Latest posts by Frank Mesaros (see all)

Leave a Reply

Your email address will not be published. Required fields are marked *