Increased visceral adipose tissue (VAT) and intrahepatic triglyceride (IHTG) are important risk factors for the development of type 2 diabetes in subjects with obesity. The relative contribution of these ectopic fat depots to cardiometabolic risk differs between populations, depends on the degree of obesity and the level of cardiorespiratory fitness, and is difficult to dissect because VAT and IHTG typically covary. The aim of this study was to evaluate the effect of an isolated increase in VAT or IHTG on insulin sensitivity and insulin secretion in apparently healthy normal-weight Asian subjects. Total body fat (dual X-ray absorptiometry), VAT and IHTG (magnetic resonance), insulin sensitivity (4-h hyperinsulinemic-euglycemic clamp), beta cell responsivity and insulin secretion rate (3-h mixed meal with mathematical modeling), and cardiorespiratory fitness (maximal oxygen consumption [V̇O_2max]) were evaluated in groups of lean subjects with low or high VAT (687 ± 94 vs. 1,279 ± 197 ml, matched for IHTG; n = 13 each) and low or high IHTG (1.7 ± 0.3 vs. 6.7 ± 2.0%, matched for VAT; n = 15 each). All groups were matched for age, sex, total body fat, and V̇O_2max. High-VAT subjects had ~25% lower insulin sensitivity, ~20%–40% greater beta cell responsivity and insulin secretion rate, ~35% greater fasting triglyceride concentration, and ~40% lower adiponectin concentration than low-VAT subjects (all P < 0.05). No differences were observed between low-IHTG and high-IHTG subjects. Accumulation of excess fat in the intra-abdominal area is more strongly associated with metabolic dysfunction than accumulation of liver fat in lean Asians without diabetes.