In the last decades, the prevalence of obesity has increased in the Taiwanese population. This has the potential to impact on the risks of cardiovascular diseases and diabetes. This study investigated trends in the changes in several indices of obesity in the last decade, and the relationship between blood pressure (BP) and these obesity indices available in Mei-Jaw Corporation health-screening data from 1996/1998 to 2006. Three cross-sectional surveys among healthy individuals ages 20-59 years, in which 14,362 subjects examined in year 1996, 17,368 in 1998, and 28,524 in 2006, were included in the analysis. Body weight and height data were available from 1996, whereas %body fat, waist circumference and waist-hip ratio (Whratio) were only available from 1998 onwards. We found that the association between systolic BP and body weight, body mass index, %body fat, Whratio and waist became stronger for both men and women in 2006 than 1996 after adjustment for age, education level, alcohol intake, smoking and betel nut chewing. In contrast, non-obese people seemed to have lower diastolic BP in 2006 than in 1996. This trend is consistent irrespective of the index of obesity used. Among healthy individuals, the average values for the obesity indices increased in men but remained similar in women. However, in both men and women, the relationship between obesity and BP has changed. Further research is required to investigate the impact of these intriguing changes in the associations on the risk of cardiovascular diseases in the Taiwanese population.