Scrapie is a degenerative disorder of the central nervous system of small ruminants. Scrapie in sheep appears to be controlled by genetic factors, with polymorphisms at codons 136, 154 and 171 of the PrP gene locus being the determining parameters (Hunter et al., 2005). Individual PrP genotypes are detected primarily with blood or ear notch tissue samples. Increasingly strict regulations on food safety and public hygiene require new, practical, animal friendly methods for large scale implementation. The first aim of this study was to develop a novel genotyping method using DNA extracted from milk somatic cells from individual animal samples. The second aim was to develop a quick, easy and accurate method for assessing the prevalence of undesirable genotypes within each flock using bulk milk.