The difficulties with using nonhuman primate species such as rhesus macaques and baboons have led us to investigate the common marmoset (Callithrix jacchus) as an alternative preclinical model for transplantation research. This requires reliable methods of detecting alloreactivity between donor and recipient pairs, particularly if colonies are inbred and share just a few common alleles for leucocyte antigens. We firstly identified marmoset major histocompatibility complex (MHC) Class II DRB genes (Caja-DRB*W1201, Caja-DRB1*03, Caja-DRB*W16) using sequence-based typing techniques. Genomic DNA (n= 49) was extracted from whole blood or spleen tissue. Exon 2 of target genes was amplified by PCR using primers specific for known marmoset alleles, and then sequenced using ABI PRISM® Big Dye Terminator technology and Assign sequence analysis software. DRB*W1201 was universally present. Eight DRB*W16 alleles and five DRB1*03 alleles were identified in this colony. We also identified two previously unreported DRB*W16 alleles, and confirmed inheritance of these alleles within several sibling groups. Subsequently, we investigated whether matching at MHC Class II DRB loci alone could predict alloreactivity, as assessed in vitro by two-way mixed lymphocyte reactions (MLRs). Fully DRB-matched, partially mismatched and fully mismatched animal pairs were prospectively chosen. MLR was performed using mononuclear cells (MNC) isolated from whole blood by density gradient separation. T-cell proliferation after 5-day culture was measured by 3H-thymidine incorporation. Combined MNC from fully mismatched and partially mismatched animal pairs exhibited significant in vitro T-cell proliferation above single cell controls (P < 0.01). MNC from fully DRB-matched (but unrelated) animal pairs exhibited no proliferation compared with controls (P= 0.3). Using DRB genotyping, suitably alloreactive donor–recipient pairs may therefore be rapidly and accurately identified for use in further studies of cellular and solid organ transplantation.