In this work we show the problems we have found, in the performance of a diagnostic protocol for the 136, 154 and 171 codons of the PrnP ovine gene based on RT-PCR, when mutations exist in the adjacent nucleotides of these positions. A total of 90 individuals belonging to 3 Spanish (Xalda, Rubia del Molar and Colmenareña) and 3 Burkina Faso sheep breeds (Sahel, Djallonké and Mossi) were genotyped. Only 3 alleles (ARQ, ARR y AHQ) were found in the Burkinabé breeds. Diagnostic could not be carried out on codons 136 and 171 in 3 Burkinabé individuals. A total of 410 base pairs of the PrnP gene including codons 136, 154 and 171 were sequenced allowing the identification of polymorphisms on codons 138, 143 and 172. The identified polymorphisms affected diagnostic performance. Programmes using the PrnP genotype as selection criterion could also be affected.