Introduction: The increasing prevalence of childhood obesity and related disorders have become a major health concern, prompting calls for the intervention strategies. The aim of the present study is to describe trends in cardiovascular risk factors in Iran. Materials and Methods: Data on cardiovascular risk factors in 2000, 2003 and 2006 in a cohort of subjects, aged 2-17 years in the TLGS group were used. To assess secular trends, Body Mass Index, waist circumference, waist to hip ratio, systolic and diastolic blood pressure, total cholesterol, low density lipoprotein  cholesterol, high density lipoprotein cholesterol, triglycerides and fasting blood sugar were compared between the three phases. Results: Waist to hip ratio in all age groups of boys increased significantly in phase two(P=0.01,0.0001,0.001 respectively). Also, blood pressure levels continued to decrease in all subjects. There were significant decreases in total cholesterol, low density lipoprotein and triglycerides in some groups. A significant increase was observed in waist circumference in 7-12 year old boys in phase two (P=0.0001, 0.001 respectively). The prevalence of overweight increased in boys in phase two (P=0.001) and in girls in phase three (P=0.05). Obesity increased significantly in boys in phase three (P=0.001) and in girls in phase two (P=0.001). Hypercholesterolemia increased in both sexes in phases two and three (P=0.001, 0.01 respectively) and HDL<35mg/dl increased in boys (P=0.001). Conclusion: Increase in cardiovascular risk factors in emphasizes the urgent need for interventions.