Major histocompatibility complex (MHC) class II genes play a major role in the vertebrate immune response, and are useful indicators of adaptive variation in wild populations. We developed PCR primers for part (114 bp excluding primers, coding for 38 amino acids) of the second exon of two expressed MHC class II genes (designated A and B) in the natterjack toad Bufo calamita. We detected five alleles in 200 individuals from range-edge populations in Britain, two of which we ascribed to locus A and three to locus B. Seven out of 10 variable amino acid sites were associated with antigen binding. In a discrete study population we detected a significant excess of non-synonymous substitutions at antigen binding sites, and a heterozygote excess, at locus A indicating that this gene is under positive selection. However, there were no significant excesses of non-synonymous substitutions or heterozygotes at locus B.