Susceptibility to scrapie is known to be associated with polymorphisms at the prion protein (PrP) gene, and this association is the basis of current selective programmes implemented to control scrapie in many countries. However, these programmes might have unintended consequences for other traits that might be associated with PrP genotype. The objective of this study was to investigate the relationship between PrP genotype and coat colour characteristics in two UK native sheep breeds valued for their distinctive coat colour patterns. Coat colour pattern, darkness and spotting and PrP genotype records were available for 11 674 Badgerfaced Welsh Mountain and 2338 Shetland sheep. The data were analysed with a log-linear model using maximum likelihood. Results showed a strong significant association of PrP genotype with coat colour pattern in Badgerfaced Welsh Mountain and Shetland sheep and with the presence of white spotting in Shetland sheep. Animals with the ARR/ARR genotype (the most scrapie resistant) had higher odds of having a light dorsum and a dark abdomen than the reverse pattern. The implication of these associations is that selection to increase resistance to scrapie based only on PrP genotype could result in change in morphological diversity and affect other associated traits such as fitness.