Intra-abdominal adiposity is associated with unfavorable serum lipid profiles (high total cholesterol or triacylglycerol, and low high-density lipoprotein cholesterol) in obese people. However, the relation in mainly nonobese Japanese population is not well known. We examined the relationship between intra-abdominal adiposity measured by ultrasonography and body fat distribution with serum lipids in Japanese people living in an island in western Japan. Mainly nonobese healthy individuals (98 men, 72 premenopausal and 182 postmenopausal women) aged between 33 and 69 years were examined. Accumulation of intra-abdominal fat (Pmax) and abdominal subcutaneous fat (Smin) was measured by ultrasonography. We also measured triceps and subscapular skinfold thicknesses, and the concentrations of total cholesterol, triacylglycerol and high-density lipoprotein (HDL) cholesterol. In men and postmenopausal women, Pmax correlated significantly with the majority of serum lipids after adjusting for age, body mass index and smoking habit. In premenopausal women, Pmax correlated significantly with only total cholesterol, but marginally with triacylglycerol and HDL/total cholesterol ratio after adjustment. Our findings suggest that intra-abdominal adiposity is related to unfavorable lipid profile in both genders among mainly nonobese Japanese population.