Regarding routine microscopic methods, the permanent stained smear is the most important technique for recovering trophozoites and cysts. The chart below shows some differentiating characteristics between E. histolytica and the non-pathogenic amoebae trophozoites previously mentioned. As you can see, trophozoites are often difficult to distinguish from one another, so it is always best to base diagnoses on the cyst form, if possible.
Nuclear characteristics given are the peripheral chromatin (around the membrane of the nucleus) and the karyosome, which is the central chromatin that appears as a spot or blotch near the center
Images are of trichrome-stained organisms (not a differential stain - blue, green, and pink colors vary among structures), and sizes are given. Still, images are not relative to one another.
Table 4. Differentiating E. histolytica Trophozoites from the Commensal Amoeba Trophs.| Organism | Image | Nucleus | Cytoplasm |
| Entamoeba histolytica 12–60 μm (usual is 15–20 μm) | 
(7) | Single Chromatin: finely granular and evenly distributed around periphery of nucleus. Karyosome: small and central | Finely granular "ground glass" appearance May contain bacteria or RBC's |
| E. coli 15–50 μm (usual is 20–25 μm) | 
(8) | Single Chromatin: clumped and uneven around periphery Karyosome: large, may be diffuse, may be eccentric or central | Granular Usually vacuolated Can contain bacteria, yeast and other debris |
| E. hartmanni 5–12 μm (usual 8–10 μm) | 
(9) | Single Chromatin: even, may appear as a solid ring Karyosome: small and compact; central or eccentric | Finely granular |
| Endolimax nana 6–12 μm | 
(10) | Single Chromatin: no peripheral chromatin usually seen Karyosome: large and blot-like, may take up a large portion of the nucleus | Granular, may be vacuolated |
| Iodamoeba butschlii 8–20 μm (usual 12–15 μm) | 
(11) | Single Chromatin: usually no peripheral chromatin Karyosome: large (occasionally surrounded by refractile granules) | Granular; may be vacuolated |
