The viability of 4 human isolates of Giardia intestinalis cysts using either the fluorogenic vital dyes fluorescein diacetate (FDA) and propidium iodide (PI) or in vitro excystation was assessed. Whereas viable cysts, as defined by in vitro excystation were present in each of the 4 isolates, cysts from only 3 of the 4 isolates took up the vital dyes. FDA consistently over-estimated cyst viability whilst PI under-estimated non-viable cysts when compared with in vitro excystation. Following in vitro excystation, both FDA and PI stained a proportion of unexcysted cysts indicating that FDA stained cysts which were incapable of excystation, whereas PI did not stain all cysts which were incapable of excystation. One human cyst isolate, which underwent in vitro excystation, could not be stained with either FDA or PI. In the absence of currently more specific fluorescent indicators of viability, PI alone could be used to determine the lower limit of nonviability in positive water-related samples, where small numbers of cysts are to be expected.