If routine microscopic methods are used to diagnose Giardia, multiple stool samples may need to be examined since cysts are often shed intermittently. Recovering trophozoites is more difficult since they adhere to the mucosa. Therefore, other methods, such as the string test or duodenal aspirate, may be more useful.
Since only a trophozoite form exists for most Dientamoeba, a fresh stool is essential. Permanently stained slides are recommended instead of direct wet preps because these organisms may be complex to recognize.
Table 6 shows some means of differentiating the trophozoites of the two pathogens from some of the more common non-pathogens.
Table 6. Differentiating Giardia and Dientamoeba Trophozoites from Commensal Trophozoites.| Organism | Image | Nuclei # | Other Features |
| Giardia duodenalis Pear shaped Length: 10–20 μm;
Width: 5–15μm | 
(19)
(19) | 2 (not visible if unstained) | A total of 8 flagella but they are often difficult to see Sucking disk |
| Dientamoeba fragilis Shaped like an amoeba Size: 5–15 μm | 
(20)
(20) | 40% have 1 nucleus; 60% have 2 | Internal flagella are not visible; granular or vacuolated cytoplasm |
| Chilomastix mesnili Pear shaped Length: 6–24 μm
(usual 10–15 μm)
Width: 4–8 μm | 
(21) | 1 nucleus | 4 flagella total |
| Pentatrichomonas hominis | 
(22) | 1 nucleus | 3–6 flagella Undulating membrane |
