The Major Histocompatibility Complex (MHC) plays an essential role in the immune response of vertebrates. Genes within the MHC region are traditionally classified into three classes (Class I, II and III) based on the organisation of the human MHC, where the gene dense Class III region separates the Class I and II regions encoding for genes involved in antigen presentation. The Class III regions of mammals, aves, amphibia and teleost fishes have been previously investigated, with major differences in Class III gene content noted between aves and mammals. However, to date, there is no published data investigating this region in reptiles, which hold a key phylogenetic position in the genome evolution of vertebrates. This study aims to provide insight into the Class III region in a reptile, the Australian central bearded dragon, Pogona vitticeps (Agamidae) and to develop a comparative map in order to investigate the evolution and conservation of this region throughout vertebrates. Through analysis of the recently assembled P. vitticeps genome and physical mapping of Class III genes, we have revealed the Class III region of P. vitticeps contains at least 38 human Class III orthologues distributed over nine sequence scaffolds and resides on the long arm of chromosome 2. The P. vitticeps Class III region does share some conserved synteny with the human Class III region; with the presence of some genes (for example SAPCD1, VWA7, LSM2 and VARS) clustered together in both species. However, some rearrangements have occurred. Class III-containing bacterial artificial chromosome (BAC) clones were end sequenced in an attempt to join the sequence scaffolds and gain a better assembly of the region. Analysis of BAC-end sequencing data has revealed the presence of non-Class III genes within the P. vitticeps Class III region, resulting in what appears to be a greatly extended Class III region within this agamid. This expanded Class III region, is in stark contrast to the severely restricted Class III region of aves (comprising of a single gene, C4) and the well conserved gene content of the Class III region observed between frog and mammals.