No information is available to date on the different allelelic structures of the chicken MHC class I (BF2) and beta2m proteins. To elucidate the structure, new allelic beta2m and five different BF2 genes were expressed solubly and purified in a pMAL-p2X/E. coli TB1 system. The 2D structure was detected by circular dichroism (CD) spectroscopy, and the 3D structures of their peptide-binding domain (PBD) were analyzed by homology modeling. The sequence lengths of the alpha-helix, beta-sheet, turn, and random coil in the five BF2 proteins were 69-73 aa, 67-72 aa, 35-37 aa, and 94-98 aa, respectively. The new beta2m protein displayed a typical beta-sheet. Homology modeling of the different BF2 and beta2m proteins demonstrated similarities to the structure of human and rat MHC class I proteins. The 3D structure, however, revealed that the BF2 and beta2m structures were unique. The correct refolding of recombinant BF2 and beta2m proteins might be a powerful tool to further detect antigenic peptides.