AIMS/HYPOTHESIS: Genome-wide association studies have identified novel WHR and BMI susceptibility loci. The aim of this study was to elucidate if any of these loci had an effect on quantitative measures of glucose homeostasis, including estimates of insulin release and insulin sensitivity in an epidemiological setting. METHODS: By applying an additive genetic model, 14 WHR-associated gene variants and 18 BMI-associated variants were investigated for their relationships with glucose-related metabolic traits in treatment-naive individuals from the population-based Inter99 study sample (n¿=¿6,039). RESULTS: Of the variants associated with BMI, the QPCTL rs2287019 C allele was associated with an increased insulinogenic index of 7.4% per risk allele (p¿=¿4.0¿×¿10(-7)) and increased disposition index of 5.6% (p¿=¿6.4¿×¿10(-5)). The LRP1B rs2890652 C allele was associated with insulin resistance, showing a 3.3% increase (p¿=¿0.0011) using the HOMA-insulin resistance (HOMA-IR) index and a 2.2% reduction (p¿=¿0.0014) with the Matsuda index. Of the variants associated with WHR, LYPLAL1/SLC30A10 rs4846567 G allele carriers showed a 5.2% lower HOMA-IR (p¿=¿0.00086) in women, indicating improved insulin sensitivity. Female carriers of the VEGFA rs6905288 A allele were insulin resistant, with a 3.7% increase in HOMA-IR (p¿=¿0.00036) and 4.0% decrease in Matsuda index (p¿=¿2¿×¿10(-4)). CONCLUSIONS: Our correlative findings from analysing single-locus data suggest that some variation in validated BMI and WHR loci are associated with either increased or decreased insulin sensitivity and thereby potentially with metabolically healthy or metabolically unhealthy subsets of obesity. The results call for testing in larger study samples and for further physiological exploration of the possible metabolic implications of these loci.