C-reactive protein (CRP), a nonspecific marker of inflammatory status, is associated with cardiovascular disease (CVD) risk factors and the late occurrence of heart disease in adults. However, few studies assess the plasma CRP levels in healthy children. The purpose of this study is to evaluate the relationship between plasma CRP levels and anthropometric and lipid characteristics among children in Taiwan. After a multi-stage sampling of 85 junior high schools in Taipei, we randomly selected 835 children (410 boys and 425 girls) aged 12 to 16 years. Anthropometric and lipid profiles, including total cholesterol, triglyceride, high-density lipoprotein cholesterol (HDL-C), and lipoprotein (a) were measured. We also calculated low-density lipoprotein cholesterol levels and the total cholesterol-to-HDL-C ratio as shown on the atherosclerotic index. In both genders, plasma CRP levels were significantly positively correlated with anthropometrics measures and inversely correlated with HDL-C levels. After adjusting for age, cigarette smoking, alcohol consumption, heart rate, and puberty development, children in the fourth quartile CRP subgroups were heavier and had significantly higher body mass index (BMI) and lower HDL-C levels than children with nondetected CRP. In multivariate regression models, CRP was significantly negatively associated with HDL-C levels even after adjusting for BMI in both genders. In this study, anthropometrics measures, especially BMI, were positively associated with plasma CRP levels. Furthermore, elevated CRP levels were associated with adverse lipids profiles. These data suggest that elevated plasma CRP levels might be associated with CVD risk factors that may be related to the late development of CVD in some Taiwanese children.