The European polecat, Mustela putorius, occurs almost throughout Europe. However, there is a lack of data on the ectoparasite fauna and the potential role in the circulation of tick-borne pathogens (TBP) of this mustelid species. The aim of this study was to investigate whether M. putorius contributes to the maintenance of TBP in Germany. DNA samples extracted from spleen tissue of 117 M. putorius, which had been collected mainly in North-western Germany from 2012 to 2015, were tested by real-time and conventional PCRs for Anaplasma phagocytophilum, Babesia spp., Bartonella spp., Candidatus Neoehrlichia mikurensis (CNM) and Hepatozoon spp. In addition, 200 randomly selected engorged Ixodes hexagonus ticks (100 females and 100 nymphs) collected from 39 of the 88 M. putorius were tested for these TBPs, except for Hepatozoon spp., and additionally for Borrelia spp. and Rickettsia spp. Three of six pathogens were detected in the spleen tissue of the 117 M. putorius: A. phagocytophilum (n = 5; 4.3%), Babesia cf. odocoilei (n = 1; 0.9%) and CNM (n = 1; 0.9%), including one case of co-infection (A. phagocytophilum and CNM). Ixodes hexagonus ticks tested positive only for Bartonella spp. (26/200 ticks; 13.0%) which were detected exclusively in adult female ticks. Sequencing revealed the presence of Bartonella taylorii and uncultured Bartonella spp. The results suggest that M. putorius neither seems to serve as the main reservoir nor plays an important role in maintaining TBPs in Germany but may rather contribute to the dilution of these pathogens. However, M. putorius contributes to the maintenance of tick populations, especially of I. hexagonus. The high prevalence of Bartonella spp. in I. hexagonus ticks may suggest a certain importance of this tick species in the maintenance of these bacteria in nature.