We investigated the importance of the MHC-constitution (major histocompatibility complex-constitution) on the endoparasite load in free-range hairy-footed gerbils (Gerbillurus paeba) in the southern Kalahari Desert. While the number of alleles of the duplicated DRB exon 2 gene had no significant effects on the individual status of being ‘not infected’ or ‘infected’ and on the number of helminth morphotype infections per individual, it significantly affected the faecal egg count values. One allele (Gepa-DRB*15) was only found in uninfected mice. Our results support the hypotheses that MHC polymorphism in G. paeba is maintained by pathogen-driven selection. The present study is the first investigation on associations between duplicated DRB gene loci and the parasite load in mammals.