The allele, genotype, and haplotype frequencies among 837 Polish Holstein-Friesian cattle were determined at two regulatory indel polymorphisms of the PRNP gene. Allele frequencies at the 23 bp indel promoter polymorphism were 0.622 (del) and 0.378 (ins), with 0.613 and 0.387 in sires and 0.633 and 0.366 in dams. Allele frequencies at the 12 bp indel intron polymorphism were 0.527 (del) and 0.473 (ins), with 0.529 and 0.471 in sires and 0.543 and 0.456 in dams. Four haplotypes were identified in this population (23-12del, 23-12ins, 23del-12ins, and 23ins-12del). Haplotype 23-12del occurred most frequently in both sire and dam groups. Comparative analysis of Polish Holstein-Friesian and German Holstein populations revealed a similar genetic structure for the 23 bp indel polymorphism and a significantly different one for the 12 bp indel polymorphism. In allele and haplotype analysis, significant differences were observed between the Polish Holstein-Friesian population and a BSE-free German Holstein population.