A large intramyocellular lipid (IMCL) pool is associated with early pathogenesis of insulin resistance and type 2 diabetes. Studies from mother-offspring cohorts indicate that, like obesity and metabolic traits, IMCL is also highly heritable. However, here have been not many studies on the effect of genetic variation on IMCL. Although a number of genome-wide association studies (GWAS) have established associations between several genetic loci and metabolic disorders, it is not yet known if these loci also contribute to IMCL levels, and help explain ethnic difference in IMCL levels. In this study, we examined the ethnic differences (Indian, Malay and Chinese) in IMCL in Singaporean children and the genetic risk variant(s) associated with these differences.