Primate molecular genetics, cytogenetics and genomics currently form a highly dynamic field of research. This has not occurred simply because of advances in technology. It is largely a consequence of the key insight that many aspects of human genome functioning can be better understood when knowledge about the conservation of, and changes in, genome organization during the course of evolution is integrated. Studies of our closest phylogenomic relatives, the nonhuman primates, can provide detailed information on the molecular mechanisms that shape the human genome. Consequently the chimpanzee genome project put forth the first chimpanzee draft sequence and its alignment with the human reference sequence in December 2003. Including review articles and original investigations, this Cytogenetic and Genome Research single topic issue bundles various different perspectives and provides a broad overview of the present knowledge about molecular cytogenetics, genome organization and evolution of primates. It will be of great interest to researchers and geneticists in the fields of primatology, anthropology, molecular phylogeny, evolution, human genetics and genome research.