We investigated the relationships between amino acid polymorphisms of the prion protein (PrP), restriction fragment length polymorphisms (RFLP) of the PrP gene and the incidence of natural scrapie in Japan. Six variant alleles of the PrP gene were found in healthy sheep. Based on the substitutions at codons 112, 136, 154 and 171, these allelic variants were designated PrP MA~Q, PrP TA~Q, PrP Mv~Q, PrP MAHQ, PrP ~ARR and PrP MARry. Each RFLP haplotype (elhl, elh2 or e3hl) consisted of multiple alleles including PrP MARQ. Three of these variant alleles were found in scrapie-affected Suffolk sheep. PrP ~A~Q was associated with high disease incidence, PrP TARQ and PrP MAR~ were associated with low disease incidence. We found that one scrapieaffected Suffolk was homozygous for PrP uARr~ and four prpS°-positive Suffolks carried PrP MvRQ. Both of two scrapie-affected Corriedales and two out of three scrapie-affected cross-breeds between Suffolk and Corriedale carried PrP MA~n, suggesting that this allele associates with high incidence of scrapie in Corriedale and its cross-breeds.