Habitat loss and attendant fragmentation threaten the existence of many species. Conserving these species requires a straightforward and objective method that quantifies how these factors affect their survival. Therefore, we compared a variety of metrics that assess habitat fragmentation in bird ranges, using the geographical ranges of 127 forest endemic passerine birds inhabiting the Atlantic Forest of Brazil. A common, non-biological metric - cumulative area of size-ranked fragments within a species range - was misleading, as the least threatened species had the most habitat fragmentation. Instead, we recommend a modified version of metapopulation capacity. The metric links detailed spatial information on fragment sizes and spatial configuration to the birds' abilities to occupy and disperse across large areas (100,000+ km(2)). In the Atlantic Forest, metapopulation capacities were largely bimodal, in that most species' ranges had either low capacity (high risk of extinction) or high capacity (very small risk of extinction). This pattern persisted within taxonomically and ecologically homogenous groups, indicating that it is driven by fragmentation patterns and not differences in species ecology. Worryingly, we found IUCN considers some 28 of 58 species in the low metapopulation capacity cluster to not be threatened. We propose that assessing the effect of fragmentation will separate species more clearly into distinct risk categories than does a simple assessment of remaining habitat.