In total 28 samples of 14 tree species were collected from 13 localities of Slovakia during the research of ciliate communities in decaying wood mass in 2001-2004. Generally 58 ciliate species (Protozoa: Ciliophora) were determined in our samples and 9 species were recorded in Slovakia for the first time. Apart from the species diversity the research has included analyses on structure of systematic and feeding groups, genus-species relationships and forming the communities in dependence on tree species. Colpodids predominated in systematic categories and bacteriovores were dominant in feeding groups. The maximum of species (8) was noted in the genus Colpoda. Hierarchical classification based on identity of ciliate species on trees has differentiated two large groups of tree communities. However the tree species probably does not seem to play a very important role in forming ciliate communities. Even no special relation (or differences of species spectrum) has been proved between deciduous and coniferous trees.