School-based fitness testing has not been well examined in relationship to cardiometabolic risk factors in schoolchildren. PURPOSE: To determine the relationship between physical fitness, blood lipids and circulating inflammatory biomarkers independent of body mass index (BMI) in school-aged children. METHODS: Phlebotomy was performed on 278 socioeconomically and racially diverse children (11.4 ± 1.6 yr; 51% female; 36% Caucasian, 30% Hispanic, 8% Asian, 7% Black, 19% other; 70% free/reduced lunch) to measure blood lipids (total cholesterol, triglycerides, HDL, LDL, VLDL) and biomarkers of inflammation (IL-6 and CRP). Height and weight were measured to determine the child's BMI-for-age category (overweight/obese vs. normal weight) based on CDC growth charts. Schools provided data on cardiovascular physical fitness as measured by the shuttle run. Linear regression analyses were used to examine the effect of fitness and weight status on blood lipids after controlling for the covariates of gender, age, ethnicity, free/reduced lunch, and pubertal status. RESULTS: Forty-five percent of children examined were overweight/obese, 50% "did not pass" the shuttle run (unfit), and 30% had one or more blood lipids that fell outside of the healthy range. Fifty percent of the fit children and 60.5% of the unfit children were overweight/obese, respectively. Triglycerides, VLDL, CRP and IL-6 were higher in both unfit students and overweight/obese students, while HDL was lower in these groups (P<0.001 for all). HDL levels were associated with both fitness and weight status (B=3.7, P<0.05 and B=-4.4, P<0.01, respectively). IL-6 was associated with lower fitness (B=-0.29, P<0.01) but not weight status. When stratified by weight status, fitness was associated with lower triglycerides (B=-0.37, P<0.001), VLDL (B=-0.37, P<0.001), and CRP (B=-0.12, P<0.001) in overweight/obese children, while there was no effect of fitness on these variables in normal weight children. CONCLUSION: A simple school-based endurance fitness test is associated with metabolic risk factors in a diverse group of overweight/obese school-aged children. These results suggest that it may be possible to identify overweight/obese children in a community setting who are at increased cardiometabolic risk based on school-based fitness testing.