Non-human primates are often used in biomedical research, and the application of these animals as a model in immune-related diseases necessitates the characterisation of their MHC system. In particular, the MHC class II regions of the chimpanzee (Pan troglodytes), the rhesus macaque (Macaca mulatta)and the common marmoset (Callithrix jacchus) have been subject of molecular biological studies in recent years. In this study the emphasis was on MHC class II genes of another macaque species, Macaca fascicularis(crab eating macaque or cynomolgous monkey). The exon 2 of the Mhc-DQB gene (Mafa-DQB) was sequenced in each of a random panel of 60 non-pedigreed cynomolgous monkeys. This resulted in the detection of 23 Mafa-DQB1alleles that had not previously been published. In addition, unreported alleles were found in chimpanzees, rhesus macaques, orang-utans (Pongo pygmaeus) and stump-tailed macaques (Macaca arctoides), of which a few individuals were included in this study. Phylogenetic analyses confirm the trans-species model of evolution of the MHC-DQBlineages, in which a group of major alleles is passed on in the phylogeny, and has led to the sharing of allelic lineages by different species of non-human primates. The sharing of alleles is observed only for closely related macaque species. Furthermore, this manuscript provides an overview of all published, and whenever necessary corrected, non-human primate Mhc-DQB exon 2 alleles.