We examined the communities of bacteria and fungi associated with the cloaca of adult House Sparrows (Passer domesticus) to investigate whether microbes could be transferred during copulation and thus represent a cost to mating. The levels of microbes in the cloacae of the male and female of eight breeding pairs were significantly correlated. The levels of microbes on the rim of the cloacal protuberance, which comes into direct contact with another bird during copulation, were similar to those inside the cloaca. These findings are consistent with microbes being transferred during copulation. Females could also receive non-cloacal pathogens during copulation, given that two of five males sacrificed had microbes within their testes, which could be incorporated into the ejaculate. Undeveloped eggs were screened for the presence of microbes, although only a low proportion (18%) was contaminated. It seems unlikely that microbial contamination is a general cause of egg failure in this species.