A particular interest in primate genetics was fueled by the release of the complete human genome sequence drafts reported in 2001 by the IHGSC and Celera Genomics. Postgenomic comparative analyses based on the complete genome sequence of the mouse started focusing on functional, evolutionary and diversity aspects of human DNA. By analyzing molecular character states in the representatives of the major primate groups one is able to reconstruct the processes that shape genomes on the lineage to humans after the mouse-human divergence. Consequently, several primate genome sequences are about to be generated during Whole Genome Shotgun (WGS) sequencing projects and are already available for two representatives of the Old World monkeys and hominoids (rhesus monkey, chimpanzee). Comparative data restricted to functional genome parts of a meaningful primate sample (ENCODE project) are underway. These data will yield a definite phylogenetic framework linking the mouse, primate related eutherians and the major primate groups, which is indispensable for any analysis of character evolution. Concerning the functional site comparative genetic research in primates on molecular phenomena that control the spatiotemporal profile of the cellular RNA and protein composition will contribute to our understanding of genotype-phenotype correlations and the emergence of human specific traits.