The flow cytometry (FC) has been used to detect Giardia cysts and Cryptosporidium oocysts quantitatively and instantaneously in this study. The experimental results showed that FC is potential to become a more precise method for the detection of Giardia and Cryptosporidium in water. This study also evaluated the staining efficiencies for three commercial antibodies. After staining Cryptosporidium oocysts with direct immunofluorescent antibodies in water samples, two populations were detected in the scatter-plots (FL1 versus SSC) of the FC. The Cryptosporidium oocysts and Giardia cysts are significantly separated from other particles while stained with direct immunofluorescent antibodies produced by Meridian Diagnostics and Waterborne Inc.