Genetic susceptibility to various transmissible spongiform encephalopathies (TSEs) has been observed in many species including humans and sheep. Evidence for the presence of susceptibility genes on several bovine chromosomes has been reported. More recently, there have been reports of associations with nucleotide insertion/deletion variants within the promoter region of the Prion gene (PRNP) itself. The objective of our study was to perform a genome scan to identify genetic associations with bovine spongiform encephalopathy (BSE) susceptibility and/or resistance in European Holstein cattle. Optimized assays totaling 3072 genome-wide single nucleotide polymorphism (SNP) markers were used for genotyping. On average, there were 100 markers per chromosome with an additional 17 SNP markers in the PRNP gene locus. With 812 BSE Holstein cattle, including positive and control animals genotyped, we have determined ~ 2.5 million positional genotypes. Preliminary analysis indicates a single-marker association between a SNP (4136) in the promoter region of the Prion gene and BSE resistance (dominance effect, P = 0.025, additive effect, P = 0.0078). Further haplotype trend regression analysis was performed using haplotypes with SNPs both upstream and downstream of SNP 4136. The likelihood ratio test of the upstream haplotype was highly significant (P = 0.0089). In addition, the likelihood ratio test of the downstream haplotype was also significant, however, to a lesser degree (P = 0.0116). Our results exhibit an association with a SNP in the promoter region of the Prion gene with BSE disease resistance in European Holstein cattle. In addition, we observed significant SNP single-marker associations on three chromosomes previously reported to be associated with BSE resistance/susceptibility as well as several new chromosomes. In total, we have detected 31 SNPs with a P > 0.01 in 27 regions of interest, of which 20 SNPs have P > 0.005, 8 SNPs have a P > 0.001 and 3 SNPs have a P > 0.0005. These initial results have revealed several chromosomal regions of significant interest.