Objectives To investigate the association of serum lipids and high-sensitivity C-reactive protein (hs-CRP) with obesity in school children and to explore whether hs-CRP levels could be used to predict the presence or absence of obesity 12 months later. Methods The subjects were school children (6-11 years old) in Japan. Blood sampling and physical measurements were performed in school (2001); low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), triglycerides, and hs-CRP levels were measured. Data from children who could be followed 12 months later were analyzed. Subjects weighing 20 % or more over his/ her standard weight were regarded as obese, and the association of obesity with serum parameters was analyzed.Results Data from 612 subjects were analyzed (follow-up rate, 75.4 %). The mean of each serum parameter was significantly higher (inverse for HDL-C; lower) in obese than that in non-obese children. Logistic regression analysis for obesity at baseline showed that the odds ratio (OR) of hs-CRP was the highest [OR, 2.15; 95 % confidence interval (CI), 1.65-2.78 for an interquartile rage (IQR) increase]; the association with triglycerides and LDL-C/ HDL-C was significant. At the 12-month follow-up, the OR of high hs-CRP remained the highest of all serum parameters (2.09; 95 % CI, 1.63-2.69 for an IQR increase). Conclusions High levels of triglycerides, LDL-C/HDL-C, and hs-CRP increased the risk of obesity in school children. Hs-CRP is considered to be a better predictor of obesity 12 months later than is LDL-C/HDL-C.