The PrP genotyping of sheep for selection from the population of individuals with scrapie resistant genotypes has become a very important component of the scrapie eradication strategy. However, a limited number of sheep did not seem to possess a standard “two allele” genotype, but rather three or more PrP (prion protein) alleles (complex genotypes). One hypothesis is that these animals are blood chimerisms, due to exchange of blood with their co-twin during gestation. In this study, blood from sheep with different genotypes was deliberately mixed (mimicking chimerism in vitro) and genotyped using real-time Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism – Denaturating Gradient Gel Electrophoresis (RFLP-DGGE). At certain mixture ratios, complex genotypes were detected. This experiment shows that if the complex genotypes diagnosed in vivo are due to blood chimerism, they can to a certain extent be detected by these techniques.