This study evaluates prevalence of hypertension in 1996 and 2006, and examines the relationship between hypertension and weight of Taiwanese young adolescents. Two cross-sectional surveys, administered in 1996 and 2006, to junior-high school in Taipei were included. Anthropometric and blood pressure were measured using standard methods, and structured questionnaire was used to collect personal history and lifestyle characteristics. Overweight and obesity are defined based on Taiwan's Department of Health criteria and bases pre-hypertension and hypertension on the 90th and 95th percentile distribution of blood pressure of the population of both surveys. The prevalence of pre-hypertension in Taiwan between 1996 and 2006 increased from 12.0 to 14.4% for boys and decreased from 9.5 to 9.4% for girls. Hypertension increased from 22.8-29.7% and 12.5-20.7% for both boys and girls, respectively. In 1996, compared with normal young adolescents, the risk of hypertension for overweight was 1.8 times higher for boys and 3.4 times for girls. However, the risk of hypertension for overweight in 2006 was 1.7 times higher for boys and 1.5 times higher for girls compared with normal. Every unit increment of body mass index and waist circumference was associated with 17-27% and 6-11% risk of hypertension in both genders in 1996, and was associated with 9-13% and 4% risk of hypertension among young adolescents in 2006, respectively. The prevalence of hypertension has increased significantly in young adolescents, especially for overweight. It is necessary to enrol young adolescents in weight management programs to prevent hypertension-related co-morbidities.