Although bird-microbial interactions have become a topic of increasing research, the influence of nest-site characteristics, such as cavity orientation, on nest microbial communities in free-living passerines has not, to our knowledge, been investigated. This is despite the possibility of microbial differences explaining non-random patterns in nest-site selection and offspring quality, such as those exhibited by great tits (Parus major). We swabbed great tit nestboxes that faced either south-southwest (180-269°) or north-northeast (0-89°). Overall, 28 bacterial species and 11 fungal species were isolated, but the culturable microbial community differed substantially between different orientations-indeed nestboxes could be classified to their orientation group with high accuracy using microbial data. Nestboxes facing south-southwest had a significantly higher fungal load (typically double) than those facing north-northeast due to a higher abundance of two species, Epicoccum purpurascens and Cladosporium cladosporioides. There was no relationship between total bacterial load and orientation, although the abundance of one species, Pseudomonas veronii, was significantly lower in south-southwest boxes. The abundance of the allergen E. purpurascens explained almost 20% of the variation in offspring quality, being significantly and inversely related to chick size (high loads associated with small, poor quality, chicks). Our results provide empirical evidence for a correlation between nestbox orientation and culturable microbial load and a further correlation between abundance of one species, E. purpurascens, and offspring quality. Thus, microbial load, which is itself influenced by nest cavity parameters, could be the proximate factor that influences nest-site choice through its effect on offspring quality (and thus, overall fecundity).