Bats are widely recognised as natural reservoirs to numerous highly pathogenic zoonotic viruses. Their ability to remain clinically asymptomatic during most viral infection has presented a great challenge and opportunity to the very young field of bat immunology. The major histocompatibility complex (MHC) plays a central role in the innate and adaptive immune responses. This dissertation characterises the MHC region and MHC genes of the black flying fox (Pteropus alecto), providing the first insights into the MHC region of any species of bat. A partial MHC class I (MHC-I) region, a complete class II and complete class III region were identified from the current bat genome sequence assembly. All three bat MHC regions were highly contracted with conserved and syntenic gene content when compared to other mammals. Overall, the bat MHC resembles the ancestral architecture of the immune supercomplex. However, no MHC-I genes were identified in the bat genome. Sequencing of bacterial artificial chromosome (BAC) and cDNA clones resulted in the identification of 16 MHC-I loci, eight of which have preliminarily been classified as putative classical class I genes, more than any other species. Furthermore, a subset of the MHC-I genes contains a bat-specific five amino acid insertion within the α1 domain of the peptide-binding groove (PBG), potentially accommodating a larger and more diverse repertoire of antigens. A greater number of classical class I genes, together with the presence of a unique PBG, could potentially be one of the keys in the ability of bats to more effectively control viral infection. Twelve MHC class II genes, with orthology to class II genes from other mammals, were also identified in the bat genome. To our knowledge, this is also the first successful attempt at employing next generation sequencing technologies to resolve the highly complex and repetitive MHC region.