Experimental transmission of bovine spongiform encephalopathy to sheep has prompted the implementation of a surveillance plan of scrapie in small ruminants by the European Union in all member states. Since its start over 30,000 animals have been tested, and the first seven cases of sheep with detectable PrP(res) deposition in the central nervous system have been identified in Portugal. Notably, the pattern of PrP(res) distribution in the brainstem was different from that previously described for scrapie and consistent in all seven animals. Moreover, the profile of the electrophoretic mobility of PrP(res) after proteinase K treatment was equivalent in all cases analysed but distinct from that observed for scrapie. Notably, four animals had genotypes rarely associated with scrapie, including one animal homozygous for A(136)R(154)R(171). There were no cases found to exhibit vacuolation, a pattern of PrP(res) distribution or PrP(res) electrophoretic mobility corresponding to scrapie. These data reveal a putative atypical scrapie strain in Portugal not linked to specific Prnp genotypes.