The complicated routes by which organic material is channelled up to higher trophic levels via bacteria and protozoans is a major issue in aquatic microbial ecology. Because of the fragile nature of protists it is not straightforward to perform experimental studies of prey–predator interactions. Here we present an approach for the assessment of ciliate grazing on living heterotrophic nanoflagellates. Stationary phase cultures of a heterotrophic nanoflagellate (Cafeteria sp.) were live-stained by allowing them to take up fluorescently labelled macromolecules. Controls revealed that this label persisted for several hours. Fluorescently labelled living flagellates (FLLF) were added into enriched natural assemblages of marine oligotrich ciliates and uptake of FLLF was monitored over time. Oligotrich ciliates did not incorporate fluorescent-labelled macromolecules but a linear FLLF uptake over time was observed for 20–30 min at 20°C. Ingestion rates were 21–46 FLLF h^–1 at a concentration of about 2×10⁴ FLLF ml^–1, which corresponded to clearance rates of 0.7–0.8 l ciliate^–1 h^–1. These results are in the same order of reported ciliate grazing on phytoplankton of similar size. This method represents a direct approach to measure ciliate grazing specifically on living heterotrophic nanoflagellates.