To discern whether an association exists between specific combinations of polymorphisms of the prion protein (PrP) and natural scrapie in Cyprus goats, 250 goats were examined, including 164 histologically positive cases. Previously reported amino acid polymorphisms were detected at codons 154 (R-->H), 168(P-->Q), 220(Q-->H) and 240 (S-->P) and nucleotide alterations at codons 42 (a-->g) and 138 (c-->t). Additionally, novel amino acid polymorphisms were detected at codons 146 (N-->S or D) and 151 (R-->H) and new "silent" mutations were found at codons 179 (V,g-->t), 181 (D,c-->t) and 219 (T,c-->t). The two novel polymorphisms at codon 146 were found only in the healthy control and scrapie-negative goats. By comparison, none of the scrapie-affected goats encoded these polymorphisms.