Protozoan grazing on bacteria transfers significant amounts of organic carbon to higher trophic levels in aquatic ecosystems. Therefore, the determination of protozoan grazing rates on bacteria is necessary for estimating the efficiency of microbial loops in organic matter utilization and transformation. Currently, a variety of methods are available to measure protozoan grazing on bacteria but most of them result in serious physical perturbations of the examined samples. We describe an assay for protozoan grazing on bacteria by means of [3H-methyl]thymidine-labelled natural bacterial assemblages as a food tracer for protozoans. Using this method we determined the protozoan grazing rates on bacteria in ten Mazurian lakes in April and July, 2000. We compared the grazing rates with bacterial biomass production and the trophic state index of studied lakes.