This paper addresses the effects of habitat fragmentation on the phyllostomid bats of the Atlantic rain forest in Brazil, by comparing community structure (species richness and capture frequency) and the frequency of three bat species sampled along 36 transects encompassing six habitat categories: interiors and edges of large (>1000 ha) and small fragments (<100 ha), and the surrounding matrix of second-growth forests and areas of shade cocoa plantation. Species composition, richness and total captures were not directly affected by forest size per se, although the frequency of one dominant forest species (Artibeus obscurus) was significantly lower in small fragments compared with larger ones. The high connectivity among forest patches in the study area and the ability of some species to use the surrounding matrix of secondary forests and shade cocoa plantations possibly precludes the insularization effect. Qualitative habitat changes induced by fragmentation, such as edge formation and forest regrowth affected bat community structure; both modified habitats comprised a limited subset of the species assemblage found in the interiors of mature forests. The results presented here provide evidence of impoverished bat assemblages in man-modified habitats linked with deforestation and overall disturbances related with forest fragmentation.