Until June 2004, thirty-eight scrapie cases with unusual features, designated Nor98, have been diagnosed in Norway. This study investigated the distribution of PrP genotypes among Nor98 cases, their flock-mates and a random sample of Norwegian slaughtered sheep. The PrP genotype distribution of Nor98 cases differed markedly from that of previous cases of classical scrapie. A leucine/phenylalanine polymorphism at codon 141 with hitherto unknown significance to scrapie was strongly associated with Nor98 cases. Twenty of 38 (52.6 %) cases were either homozygous or heterozygous for phenylalanine at codon 141. In contrast, this allele was present in only 10.5 % of the flock-mates and 4.5 % of the random sample of slaughtered sheep. Moreover, the H(154) allele was represented in 24 of 38 (63.2 %) of Nor98 cases, as opposed to 27.0 % of Nor98 flock-mates and 17.0 % of the slaughtered sheep.