The presence of haemoparasites from the Order Piroplasmida and the genera Bartonella and Trypanosoma was assessed in the blood of 60 bats, belonging to 7 species, inhabiting sites across Cornwall in southwest England. DNA extracted from macerated heart tissue was incorporated into taxon-specific polymerase chain reactions (PCRs) and amplification products were sequenced as a means of identifying, or assigning an identity, to detected haemoparasites. A Piroplasmida species was detected in 6 Pipistrellus spp., whereas Bartonella infections were detected in 5 bats belonging to 4 different species. Trypanosoma dionisii was detected in 1 Pipistrellus spp. Phylogenetic inference from alignment of a partial 18S rRNA-encoding gene sequence of the pipistrelle-associated Piroplasmida species with homologous sequences available for other members of the Order indicated that this organism was unique but specifically related to members of the genus Babesia, a phylogeny that would be in keeping with the organism being Babesia vesperuginis. Alignment of partial citrate synthase gene sequences from the bat-associated bartonellae revealed 5 distinct genotypes that were probably derived from 2 distinct Bartonella species. The study demonstrates the utility of molecular methods for detecting haemoparasites in dead bats and provides, for the first time, tangible identities for bat-associated Babesia and Bartonella species.