Bats are presumed primary hosts of trypanosomes of the subgenus Schizotrypanum , including the human pathogen Trypanosoma cruzi . As such, research on bat trypanosomes has been focused on South America, where Chagas disease is a serious issue. While the majority of European studies have been performed in the United Kingdom, there is virtually no data available for Eastern and Central parts of Europe. To address this, the present study aims to identify and assess the prevalence and pathogenicity of trypanosomes in bats sampled in the Czech Republic, Bulgaria, and Poland. Blood collected from 381 adult bats of eight species was tested for presence of trypanosomes using nested polymerase chain reactions. To assess possible impacts of trypanosome parasites on the health status of their hosts, haematological and biochemical analyses were performed for 56 greater mouse-eared bats ( Myotis myotis ) emerging from hibernacula and 36 females of the same species from summer colonies. The overall prevalence of the two trypanosome species detected ( T. dionisii and T. vespertilionis ) was 27%, with a significantly higher prevalence in the Czech Republic compared to the other countries studied. Significant differences in bat trypanosome prevalence in different European countries appear to be connected with presence or absence of possible vectors in summer roosts. No impact of trypanosomes on haematology and blood chemistry parameters was detected in Trypanosoma -positive greater mouse-eared bats. Though T. dionisii infection in bats appears asymptomatic, long-term health consequences still need to be studied in greater detail.