Honey bees are exposed to many damaging pathogens and parasites. The most devastating is Varroa destructor, which mainly affects the brood. A promising approach for preventing its spread is to breed Varroa-resistant honey bees. One trait that has been shown to provide significant resistance against the Varroa mite is hygienic behavior, which is a behavioral response of honeybee workers to brood diseases in general. Here we report the use of an Affymetrix 44K SNP array to analyze SNPs associated with detection and uncapping of Varroa-parasitized brood by individual worker bees (Apis mellifera). For this study, 22,000 individually labeled bees were video-monitored and a sample of 122 cases and 122 controls was collected and analyzed to determine the dependence / independence of SNP genotypes from hygienic and non-hygienic behavior on a genome-wide scale. After false-discovery rate correction of the p-values, six SNP markers had highly significant associations with the trait investigated (alpha < 0.01). Inspection of the genomic regions around these SNPs led to the discovery of putative candidate genes.