Patterns of cardiovascular risk factors and metabolic syndrome risk criteria in populations are not static over time. We analyzed the trends in lipid levels, blood pressure, fasting glucose and body mass index over the last two decades among children and adolescents. Two different cross-sectional studies were examined among students (ages 8-18) in 1989 (n = 1385) and in 2008 (n = 1746). Using the international cut-off points and percentiles, we identified children and adolescents with elevated blood pressure, triglycerides, fasting glucose (>= 100 mg dL(-1)), body mass index and low high-density lipoprotein cholesterol (HDL-C) levels. The prevalence of obesity has increased several folds over the last two decades. According to the international criteria, 4.3% of children were obese and 15.2% were overweight in 2008 vs. only 0.6% obese and 4.3% overweight in 1989 (P < 0.001). The prevalence of elevated systolic blood pressure also increased significantly among 8-12-year-old boys and girls (28.5 vs. 15.7%, P < 0.001). The temporal trends in fasting glucose and lipids did not correlate with the increasing prevalence of obesity with the exception of HDL-C levels. Low HDL-C (>= 10th percentile) was observed in 16.3% in 1989 vs. 21.6% in 2008 (P = 0.016). HDL-C levels decreased significantly among adolescent boys. Finally, the prevalence of metabolic syndrome by modified National Cholesterol Education Program (NCEP) criteria has doubled over the last two decades (2.2 vs. 4.5%, P < 0.001). Strategies for combating the future cardiovascular mortality should focus on the prevention of obesity, high blood pressure and metabolic syndrome among children and adolescents.