The vertical distribution of planktonic ciliates in eight strongly stratified temperate lakes was studied in summer 1998. Ciliate abundance and biomass were highest (mean 39.9 cells ml−1 and 181.9 μg C l−1) in the epi-, and lowest (mean 8.2 cells ml−1 and 97.6 μg C l−1) in the hypolimnion. The community of ciliates was dominated by five orders: Oligotrichida, Haptorida, Prostomatida, Scuticociliatida and Peritrichida. The community composition varied greatly with depth. In the epilimnion, the ciliate numbers were dominated by oligotrichs but small algivorous prostomatids, peritrichs and haptorids were also numerous. In the metalimnion, these groups were replaced by scuticociliates and mixotrophic prostomatids. In the hypolimnion species known as benthic migrants appeared. We found a positive significant correlation (p < 0.05) between ciliate numbers and Chl a and bacterial densities. Only in the hypolimnion, the correlation between ciliates numbers and Chl a was not significant.