Entamoeba histolytica must be differentiated from other intestinal protozoa such as the nonpathogenic amebas E. coli, E. hartmanni, E. polecki, E. gingivalis, Endolimax nana, and Iodamoeba bütschlii, and from the possibly pathogenic Dientamoeba fragilis (which is not an ameba but a flagellate). 

Differentiation is possible (but not always easy) based on morphologic characteristics of the cysts and trophozoites. The nonpathogenic Entamoeba dispar, however, is morphologically identical to E. histolytica, and differentiation must be based on isoenzymatic, immunologic, or molecular analysis. 

Microscopic identification of cysts and trophozoites in the stool is the common method for diagnosing E. histolytica.  This can be accomplished using:

• Fresh stool: wet mounts and permanently stained preparations (e.g. trichrome). Concentrates from fresh stool:

• wet mounts, with or without iodine stain, and permanently stained preparations (e.g. trichrome).  Concentration procedures, however, are not useful for demonstrating trophozoites.

In addition, E. histolytica trophozoites can also be identified in aspirates or biopsy samples obtained during colonoscopy or surgery.