The Blue Tit Cyanistes caeruleus prefer to use nest boxes to raise their young rather than nests in natural tree cavities. However, nest boxes provide a warm, humid microclimate that is favourable to the growth of rich bacterial communities. In this study we investigated how the bacterial community developed throughout the breeding season and whether it had any efect on egg or nestling mortality. Samples were collected across six sites and three breeding seasons at the completion of nest building, clutch completion and immediately post fedging. Bacterial counts were obtained for each sample, including a total bacterial count using non-selective media and bacterial counts on selective media for Staphylococcus spp. and Enterobacter spp, which may indicate pathogenicity to the birds. There were signifcantly more bacteria (total counts and counts for Staphylococcus spp. and Enterobacter spp. specifcally) present within the nest box at the post fedging stage compared to the two earlier stages, likely due to increased activity by the adult birds (feeding of the nestlings and defecating) and less time by the adult birds for self-preening and nest sanitation. No positive relationship was found between bacterial counts and either egg mortality, nestling mortality or brood size; however, a negative relationship between egg mortality and total bacterial count was identifed. Although somewhat unexpected, this negative relationship may indicate the presence of a greater number of symbiotic bacteria, which could ofer a greater level of protection.