A method was developed in which indirect immunofluorescence and phase-contrast microscopy are used for rapid detection and identification of Giardia cysts in raw and finished water supplies. When anti-Giardia cyst antiserum and fluorescein conjugate were applied to known Giardia cysts on membrane filters, the cysts fluoresced bright green when they were illuminated by UV light. This procedure permitted individual cysts to be quickly located even in samples heavily contaminated with other microorganisms and debris. The identity of presumptive Giardia cysts located in this way could then be confirmed by observing characteristic internal morphological features with phase-contrast microscopy. With this method, Giardia cysts were detected and their identities were confirmed in samples taken from raw and finished surface water supplies during several recent outbreaks.