Human chromosome 18 differs from its homologues in the great apes by a pericentric inversion. We have identified a chimpanzee bacterial artificial chromosome that spans a region where a break is likely to have occurred in a human progenitor and have characterized the corresponding regions in both chimpanzees and humans. Interspecies sequence comparisons indicate that the ancestral break occurred between the genes ROCK1 and USP14. In humans, the inversion places ROCK1 near centromeric heterochromatin and USP14 adjacent to highly repetitive subtelomeric repeats. In addition, we provide evidence for a human segmental duplication that may have provided a mechanism for the inversion.