High-yielding dairy cattle are susceptible to ketosis, a metabolic disease which negatively affects the health, fertility, welfare and milk production of the cow. There is a global interest in breeding for more robust dairy cattle with improved resistance to disease; however, genetic evaluations for ketosis would benefit from the additional information provided by genetic markers. Candidate genes proposed to have a biological role in the pathogenesis of ketosis were investigated in silico and a custom panel of 998 putative single nucleotide polymorphism (SNP) markers was developed. The objective of this study was to test the associations of these new markers with ketosis records, milk β-hydroxybutyrate (BHB) data and de-regressed estimated breeding values for both traits. A preliminary sample of 653 Canadian Holstein cows that had been previously genotyped with the BovineSNP50 BeadChip (Illumina Inc., San Diego, CA) and with records for producer-recorded ketosis events and milk BHB, an indicator of ketosis, were re-genotyped with the custom panel. Estimated breeding values for ketosis and milk BHB in the first and later lactations were obtained from Canadian Dairy Network (Guelph, ON) for each animal and de-regressed for use as pseudo-phenotypes along with the ketosis and milk BHB records for association analyses. Results of the association analyses suggested 51 markers in 27 unique candidate genes associated with the 2 traits studied. Genes encoding proteins involved in metabolic processes including the synthesis and degradation of fatty acids and ketone bodies, gluconeogenesis, lipid mobilization, the citric acid cycle and cholesterol biosynthesis were identified to contain SNP associated with ketosis-resistance. This work confirmed the presence of previously described quantitative trait loci for dairy cattle, suggested novel markers for ketosis-resistance and provided insight into the underlying biology of this disease.