Prion diseases are fatal transmissible neurodegenerative disorders of both animals and humans associated with prolonged incubation periods and include scrapie, bovine spongiform encephalopathy (BSE) and Creutzfeldt-Jakob disease (CJD). The arrival of variant CJD (vCJD) and the recognition that it is causally related to BSE, to which there has been widespread dietary exposure, has lead to considerable public health concerns. According to the protein-only hypothesis, prions are principally or entirely composed of an abnormal isoform (PrPSc) of host-encoded cellular prion protein (PrPC). Human prion diseases have inherited, sporadic and acquired aetiologies. The inherited prion diseases are all associated with coding mutations in the human PrP gene (PRNP) and PrP polymorphisms are known to affect susceptibility, incubation time and disease phenotype. Although PRNP is the major genetic determinant of prion disease susceptibility, it is becoming clear that other genes play an important role. Genetic studies in humans are limited by the small numbers of affected individuals and therefore to identify these genes several large mouse crosses have been analysed and multiple loci on at least eight different chromosomes now identified. To date, the regions identified are large and the identification of candidate genes remains challenging. However, the development of alternative mouse crosses offers the prospect of fine mapping, which, together with microarray analysis and increased sequence information, now makes identifying these susceptibility genes a realistic goal. Characterisation of these mouse alleles and then their human homologues may allow the identification of at-risk individuals for BSE prion infection, allow better prediction of any vCJD epidemic, and ultimately should identify new proteins and biochemical pathways which will contribute to our understanding of prion pathogenesis and provide new targets for therapeutic intervention.