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Introduction: This study presents the prevalence of cardiometabolic risk factors in a nationally representative sample of Iranian children and adolescents. Methods: This multi-centric study was conducted in 2015 among 4200 students aged 7-18 years. They were selected by multistage cluster sampling from 30 provinces of Iran. Anthropometric indices, biochemical and clinical parameters were measured. Results: The mean of weight, height, waist circumference (WC), systolic blood pressure (SBP), diastolic blood pressure (DBP), and fasting blood glucose (FBG) was higher in boys than in girls ( P < 0.05). The mean of triglyceride (TG), total cholesterol (TC) and low-density lipoprotein (LDL) levels were higher in girls than in boys ( P < 0.05). The mean of weight, height, WC, SBP, DBP, alanine transaminase (ALT) and body mass index (BMI) was higher in urban than in rural residents ( P < 0.05). Overall, 16.1%, 9.4% and 11.4% were underweight, overweight and obese. Abdominal obesity was documented in 21.6% of boys and 20.5% of girls. Low HDL-C was the most prevalent abnormality of lipid profile (29.5%) followed by high serum TGs (27.7%). Low HDL-C was more prevalent in boys than in girls (32.7% vs. 26%, respectively, P < 0.05). Prevalence of obesity and overweight were higher in girls than in boys ( P < 0.05). The prevalence of obesity and overweight, abdominal obesity, and low HDL-C were higher in urban than in rural residents ( P < 0.05). Conclusion: We found considerably high prevalence of some cardiometabolic risk factors including overweight and obesity, low HDL-C and hypertriglyceridemia in Iranian children and adolescents. The current findings underscore the necessity of intensifying health interventions for primordial and primary prevention of non-communicable diseases from early life.