Flow cytometry has found wide applications in areas like haematology and immunology, but also presents great potential in microbiology. The susceptibility of clinical isolates of Candida and Cryptococcus to antifungal compounds can be assayed by flow cytometry using fluorescent probes like FUN-1, propidium iodide and JC-1, with several advantages. Following 1 or 2 h of incubation, depending on the antifungal compound, versus 48 h of the classical methods, it is possible to establish the different susceptibility profiles. Additionally, it provides information regarding the mechanisms of action and might infer about resistance mechanisms.