Recent experiments have demonstrated that fluorogenic substrates are taken up by Giardia cysts and that an excellent correlation exists between animal infectivity and vital staining with fluorescein diacetate (FDA) for viable cysts and propidium iodide (PI) for non-viable cysts. Examination of FDA stained Giardia muris cysts with either Nomarski differential interference contrast (DIC) or brightfield (BF) microscopy revealed a direct correlation between morphologic appearance and uptake of FDA or PI. Cysts incorporating FDA were all morphologically identical and exhibited (1) a clearly delineated cyst wall, (2) the presence of a distinct space between cyst wall and cytoplasm, and (3) flagella recognizable at one pole of the cyst. Examination of PI stained cysts demonstrated the presence of well-defined nuclei, intracellular axonemes, and curved elements of the adhesive disc. The cytoplasm of PI stained cysts contained a fine granular texture as opposed to the hyaline appearance of FDA stained cysts, and no space was observed separating the cyst wall from underlying cytoplasm in the PI cyst. The correlation of fluorogenic dye uptake by cysts and their morphologic appearance provides a simple, direct, and inexpensive method for determining the viability of Giardia muris cysts which should have wide applicability in studies using environmental factors or chemical agents that may effect Giardia cyst viability.