This study compared the waist circumference (WC) measurements of Chinese children at different sites to determine the relationship between WC measurements and body fat. WC was measured at five sites in 255 subjects aged 9-19 years: immediately below the lowest rib (WC1), at the narrowest waist (WC2), the midpoint between the lowest rib and the iliac crest (WC3), 1 cm above the umbilicus (WC4), and immediately above the iliac crest (WC5). Body fat mass (FM), body fat percentage (% BF), body fat mass in the trunk (FM in the trunk), and fat percentage in the trunk (% BF in the trunk) were determined by dual-energy X-ray absorptiometry. The WCs were then compared through ANOVA with repeated measurement. The relationship of WC of each site with FM, % BF, FM in the trunk, and % BF in the trunk was examined through partial correlation. The WCs exhibited the following pattern: WC2 < WC1 < WC3 < WC4 < WC5 (p < 0.001) in males and WC2 < WC1 < WC4, WC3 < WC5 (p < 0.001) in females. The measured WCs were strongly correlated with FM, % BF, FM in the trunk, and % BF in the trunk. The WC measurements at five commonly used sites among Chinese children are different from one another. Results indicate that standardizing the anatomic point for the WC measurements is necessary.