A Guide to Special Stains: Part 1

By: Meghan McDonald

Special Stains are used in histology to identify specific organisms which are not normally distinguished during routine Hematoxylin and Eosin (H & E) staining.

There are many different types of special stains, but the most common ones are briefly discussed below:

Figure 1

Acid Fast Bacteria (AFB) is a type of mycobacterium which divides bacteria into acid fast or non-acid fast. Acid fast organisms contain a waxy or fatty layer on their surface, whereas non-acid fast bacteria does not. Due to the presence or absence of the waxy layer, the acid fast bacteria will stain a bright red, while the non-acid fast will be light blue. See Figure 1.

Congo red is a stain used to identify any amyloid present in tissues. Amyloid will stain a dark pink to red, whereas the elastic tissue will be a pale pink. Any nuclei present will appear blue. When viewed under polarized light, amyloid deposits will appear as an apple-green birefringence. It’s important for the thickness of sections to be cut at 8 to 10 µm to allow for the apple-green birefringence. See Figure 2.

Figure 2

Figure 3

Copper stain is used to identify copper pigments in liver. Copper will appear bright red to red yellow, and the nuclei will be light blue. See Figure 3.

Figure 4

Gram Stains classify bacteria as gram-positive or gram-negative depending on the thickness of their cell wall. Gram-positive bacteria, have a thicker cell wall, and will stain blue, and gram-negative bacteria, have a thinner cell wall, and will stain red. The background tissue is yellow, while the nuclei will be light red. See Figure 4.

Figure 5

Grocott’s Methenamine Silver (GMS) is used for the identification of fungi. Fungi will stain black with well-defined cell walls. The background will be green due to the counterstain, and any mucin present will be taupe to dark gray. See Figure 5.

Stay tuned for more special stains in the remaining parts of this series!


A Congo Red Study, Researchgate.net. March 2014.

AFB, Basic Fuchsin, Ellis & Zabrowarny Stain Kit, Newcomer Supply. 2018

Alcian Blue/PAS Kit, Newcomer Supply. 2018

Copper, Newcomer Supply. 2018

Elastic, Verhoeff Stain Kit, Newcomer Supply. 2018

Gomori Methenamine Silver stain, Abcam. 2018.

Gram, Brown-Hopps Stain Kit, Newcomer Supply. 2018

Histotechnology: A Self-Instructional Test, 3rd Edition, Freida L. Carson, 2009.

Iron, Gomori Prussian Blue Stain Kit, Newcomer Supply. 2018

Mucin, Mayer Mucicarmine Stain Kit, Newcomer Supply. 2018

Trichrome, Masson, Aniline Blue Stain Kit, Newcomer Supply. 2018

PAS Stain, Schiff’s Reagent, Glycogen Stain, Newcomer Supply. 2018

Reticulum, Gordon & Sweets Stain Kit, Newcomer Supply. 2018




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