Kidney stone disease is a common condition, affecting up to 10% of the population in Japan as well as in the industrial world. Calcium oxalate is major stone composition, consists of crystal and stone matrix, and arises from a combination of environmental and genetic factors. To date, considerable progress has been made identifying the metabolic risk factors predisposing to this complex disease. The familial association of calcium oxalate stone has been corroborated by numerous studies. The specific genetic and epigenetic factors have remained less clear. However genetic variations have indicated using single nucleotide polymorphism (SNP) , and recent technological advances by way of commercially available SNP array or chips, which capture common human variation across the entire genome, have been revolutionizing the study and identifying a new gene as a risk locus in idiopathic calcium oxalate kidney stone disease.