A method based on the live-staining (DAPI, FITC, DTAF) of heterotrophic flagellates was developed. These fluorescently labelled flagellates (FLF, different species) were offered as living prey in grazing experiments. The ingested differentially labelled flagellates could easily be identified in food vacuoles of protists by using the epifluorescence microscopy. We tested the method by using a filter-feeding ciliate (Euplotes vannus) and a heterotrophic dinoflagellate (Oxyrrhis marina) as predators of FLF. The food selectivity regarding different species of heterotrophic (Cafeteria, Bodo, Spumella, Oxyrrhis) and autotrophic (Chlamydomonas) flagellates was estimated from food vacuole contents of protists. Both protistan predators showed a preference for large flagellates. Grazing rates of Euplotes and Oxyrrhis on heterotrophic flagellates ranged between 2-53 flagellates per ciliate and hour and 1-31 flagellates and flagellate and hour, respectively. The method was proofed to be very useful for the quantification of trophic interactions among protists using epifluorescence microscopy, it can also be applied for studies by laser scanning microscopy and should be applicable for investigation by flow cytometry.