Background The human amylase gene (AMY1) has broad copy number (CN) variation that may associate with BMI. Methods DNA was extracted from urine (n=74) and serum (n=6) samples (‘ProFiMet’ cohort), and buccal (n=17) samples (Oral Starch Challenge [OSC] cohort), and assessed for AMY1 CN by droplet digital PCR. Association of AMY1 CN with comprehensive markers of metabolic status (ProFiMet cohort) were analysed with Pearson Correlation Coefficients (CC). For the healthy, euglycemic OSC cohort, glycemic response to OSC was analysed with independent-sample t-tests (subgroups: high AMY1 CN 9-12, n=10; low AMY1 CN 4-6, n=7). Results There were significant inverse correlations of AMY1 CN with total visceral fat volume (CC -0.33; P=0.004), and positive correlations of AMY1 CN with oral glucose insulin sensitivity score (OGIS [derived from OGTT], CC 0.26; P=0.02), serum HDL-cholesterol (CC 0.325; P=0.003), and serum adiponectin (CC 0.249; P=0.026). Linear regression multivariate analysis (adiponectin as dependent variable), showed independent association of adiponectin with AMY1 CN (Beta=0.29; P=0.03). There were no significant associations between AMY1 CN and clamp-derived M-value, homeostasis model assessment of insulin resistance (IR), hepatic endogenous glucose production, fecal floral signature or macronutrient dietary preference. Delta (mean) change in blood glucose concentration (fasting to 30-min post-OSC), was significantly greater in the high vs low AMY1 CN subgroups (mean 1.7mmol/l [SEM 0.6] vs 0.9mmol/l [SEM 0.9] respectively; p=0.016). Conclusions High AMY1 CN associates with favourable metabolic profile (lower visceral fat volume; higher serum adiponectin; enhanced glucose absorption following oral glucose and OSC), but not with whole-body or hepatic IR.