Although bats are one of the most successful and diverse of mammalian orders, studies that focus upon bat endoparasites are limited. To further knowledge of bat parasitology, pipistrelle bats (Pipistrellus pipistrellus and P. pygmaeus) were acquired from across the Greater Manchester and Lancashire region of England and examined for gastrointestinal helminths using morphological and molecular analyses†. Sixty-eight of 90 adult/juvenile bats (76% prevalence) were infected with at least 1 species of helminth and mean helminth abundance was 48·2 (+/− 7·0). All helminths were digenean trematodes and the following species were identified in 51 P. pipistrellus specimens (prevalence in parentheses): Lecithodendrium linstowi (80·4%), L. spathulatum (19·6%), Prosthodendrium sp. (35·3%), Plagiorchis koreanus (29·4%) and Pycnoporus heteroporus (9·8%). Statistical analyses, incorporating multifactorial models, showed that male bats exhibited a significantly more aggregated helminth distribution and lower abundance than females. Positive associations were observed between L. linstowi and L. spathulatum, Prosthodendrium sp. and P. heteroporus and between L. spathulatum and P. koreanus. A revised phylogeny of bat-associated Lecithodendriidae, incorporating novel L. spathulatum and Prosthodendrium sp. 28S rRNA sequences, separated the controversial clade formed by L. linstowi and P. hurkovaae. Further studies are likely to assist the understanding of bat-parasite/pathogen relationships, helminth infracommunity structures and phylogenetics.