Knowledge about the protozoan parasite fauna in voles (Arvicolinae) in Austria is rather limited, although some of these pathogens play an important role in human medicine and cause zoonoses (e.g., Toxoplasma gondii and Encephalitozoon cuniculi). Others are of relevance in veterinary medicine and have a negative economic impact (e.g., Neospora caninum). Two hundred sixty-eight common voles (Microtus arvalis) and 86 water voles (Arvicola terrestris) from the most western Austrian province, Vorarlberg, were analyzed with PCR techniques for infections with T. gondii, N. caninum, and E. cuniculi. Brain tissues of two common voles (0.7%) and of four water voles (4.7%) tested positive for T. gondii. Furthermore, analysis of four common voles (1.5%) and two water voles (2.3%) generated positive findings for N. caninum, and brain tissues of 16 common voles (6%) and six water voles (7%) tested positive for E. cuniculi. Accordingly, this study not only demonstrates the autochthonous existence of the zoonotic parasites T. gondii and E. cuniculi in voles in Vorarlberg, it also provides the first evidence of an occurrence of N. caninum in animals of the subfamily Arvicolinae, and it is an additional contribution to investigations of the sylvatic cycle of N. caninum.