The initial human and chimpanzee genome sequences have been published, and additional primate genomes, including those of gorilla and orang-utan, are in progress. With these new resources, we can now address what makes our species unique, by focusing on the underlying genetic differences associated with phenotypes. Comparative primate population genomics, including studies of structural changes, mobile elements, gene expression and functional analyses, will shed light on how natural selection and population demography are involved in the processes that lead to differences among great apes. Historically, this research has focused on the human perspective; however, we will learn much about ourselves with a focus on genomic diversity in hominoids as a group.