In adults, visceral fat accumulation is an important indicator for cardiovascular disease risk. This relationship is not fully understood in children. To determine the best predictor of cardiovascular disease risk factors among anthropometric indices such as body mass index (BMI), percent body fat (%Fat), waist-to-hip ratio (WHR), waist circumference, and waist-to-height ratio (W/Ht ratio) in Japanese schoolchildren. This study included 880 children (447 boys and 433 girls), 9-13y of age. Dependent variables were total cholesterol(TC), triglycerides(TG), high-density lipoprotein cholesterol(HDLC), low-density lipoprotein cholesterol(LDLC), atherogenic index(AI), life style related disease prevention score, and systolic(SBP) and diastolic(DBP) blood pressure. The strongest correlation was found between W/Ht ratio and the score by Pearson’s correlation analysis. Multiple regression analysis showed that significant independent correlates for the score included W/Ht ratio and %Fat. Among the anthropometric indices, W/Ht ratio was the most significant predictor for TC, TG, LDLC, AI, and the score. W/Ht ratio is the best predictor of cardiovascular risk factors in Japanese schoolchildren. We propose using W/Ht ratio for detecting cardiovascular disease risk in children.