The spatial distribution of Neotropical birds at local scales is often associated with plant successional stages and unique microhabitats such as bamboo stands and treefall gaps. Only 15% of the Atlantic Forest remains, yet this habitat is home to more than 200 endemic birds. Understanding the distribution of bird species within the Atlantic Forest can improve the test of ecological hypotheses related to habitat use and habitat selection. This study analyses the distribution of birds among different types of relief (lowlands, ravines, hillsides, and hilltops) in 41 forest fragments of different sizes (1 to 384.5 ha) within the Atlantic Forest, south east Brazil. The presence and absence data were analysed with dynamic occupancy models to determine the influence of area and topography in the distribution of bird species. Of the 169 species detected, we were able to estimate an occupancy probability of 67. Among them, relief type was an important variable for 26 species (39%). Most species showed a preference for lowlands and ravines, and some showed an association of combinations of these two reliefs with hillsides and hilltops. These preferences might be related to distribution of preferred food, nesting microhabitats, and thermoregulation. For the endemic and threatened Atlantic Forest mountain birds, the ecological association with areas of relief is a strong, and previously unsuspected, spatial distribution pattern. Our results suggest that the ecology and distribution of birds in tropical forests across hilly regions could be better understood if topography is considered. This pattern should be better investigated among other taxa in tropical forests.