Nematodes adversely affect animal health and cause serious economic losses; one option for control is the use of genetically resistant stock. There is an association between the MHC class II loci and resistance to nematode infections of sheep such as DRB1 gene. Our long-term aim is to fine-map the causative mutations but in order to design efficient and powerful experiments, we need to determine the extent of diversity at the different loci. We have therefore sequenced the second exons of all alleles at the DQA1, DQA2, DQB1, and DQB2 loci in naturally infected lambs from the Scottish Blackface breed and Texel breeds.