The aim of this study was to identify SNPs in the cattle genome associated with estimated breeding values of feet (EBVfeet) in Holstein-Friesian (HF) cows in Hungary. Foot health is of major importance in dairy cattle industry whereas claw disorders are leading to lameness and thus result in low fertility rates and productivity. Genotyping was performed using the EuroG_MDv4 microarray platform. The final database comprised 2963 animals and 59,151 SNPs. EBVfeet values have been divided into high and low groups. All calculations regarding the genetic differentiation (genome-wide and locus-specific) between high- and low-value groups for EBVfeet, linear regression, and haplotype association tests have been performed with the SNP and Variation Suite software. Thirty-nine SNPs associated with EBVfeet were determined on BTAs 3, 7, 8, 15, 21, and X. The maximum values of the identified SNPs were 0.22 for Fst_marker, 23.1 for the −log10(p) of the linear regression, and 26.3 for the −log10(p) of the haplotype association tests on BTA 3. The closest genes to SNPs associated with estimated breeding values for feet (EBVfeet) are mainly associated with tissue structure, immune response, metabolism, growth, development, transport and signaling. Our results could add additional information to the genetic programs focusing on the improvement of foot health in HF cattle.