- Cysts of Iodamoeba buetschlii vary from being nearly spherical to ellipsoidal, and measure 5-20 µm.
- Cysts contain a single nucleus that is not visible in either unstained or iodine-stained wet mounts. With permanent stains (such as trichrome), the nucleus contains a large, usually eccentric karyosome. Achromatic granules may or may not be present around the karyosome.
- An important diagnostic feature for this species is the presence of a large compact mass (vacuole) of glycogen in the cyst stage. Although this mass can be visible in unstained wet mounts, in iodine-stained preparations it takes on a darker, reddish-brown color. The glycogen vacuole does not stain with trichrome, but will still be visible as a well-defined mass.

