BACKGROUND: The association between objectively assessed sedentary time and metabolic risk factors in childhood have rarely been studied. Therefore, we examined the independent relationship between objectively assessed and self-rated sedentary time and indicators of metabolic health in Dutch and Hungarian 10-12 year olds. METHODOLOGY/PRINCIPAL FINDINGS: We performed a cross-sectional survey in primary schools. Participants were Dutch and Hungarian girls (n = 73, aged 12.2 ± 0.6 years, 18% overweight/obese) and boys (n = 69, aged 12.2 ± 0.7 years, 38% overweight/obese). Sedentary time and physical activity were assessed by the Actigraph accelerometer. TV and PC time were assessed by self-report. Adiposity indicators included body weight, height, and waist circumference (WC). Fasting plasma glucose, C-peptide, total cholesterol, low density lipoprotein cholesterol, high density lipoprotein cholesterol, and triglycerides were determined in capillary blood and summed into a metabolic risk score. Linear regression analyses were adjusted for physical activity, number of sedentary bouts and WC. Children spent on average 7.6 hours of their daily waking time in sedentary behavior and self-reported 116 ± 64 min/day watching TV and 85 ± 57 min/day using the computer. Comparing the 1(st) and 4(th) quartile of objectively assessed sedentary time, C-Peptide levels, WC and BMI were significantly higher in the most sedentary quartile, while the difference in metabolic risk score was borderline significant (p = 0.09). Comparing the 1(st) and 4(th) quartile of TV time, BMI was significantly higher in the most sedentary quartile, while the difference in WC score was borderline significant (p = 0.06). In the adjusted linear regression analysis we found no significant association of sedentary time with metabolic risk. CONCLUSIONS/SIGNIFICANCE: Although BMI and WC were higher in the most sedentary versus the least sedentary children; we found no further evidence that more sedentary children were at increased metabolic risk.