The association between the change in a central pattern of body fat and blood pressure and lipoprotein levels was investigated longitudinally in a healthy population of young males and females over 15 years. The subjects (males, n = 84; females, n = 98), participants in the Amsterdam Growth and Health Study, were measured six times between the mean ages of 13 and 27 years. As an indicator of a central pattern of body fat, subscapular/triceps skinfold ratio (S/T ratio) was used as an independent variable. Systolic blood pressure (SBP), diastolic blood pressure (DBP), total serum cholesterol (TC), high density lipoprotein cholesterol (HDL-C), and TC/HDL-C ratio were used as dependent variables. Longitudinal associations were analyzed by generalized estimating equations (GEE) in which data of the six periods of measurement were included simultaneously. Between ages 13 and 27 years, and after adjustment for the sum of four skinfolds, physical activity, smoking, and alcohol intake, the increase of the S/T ratio was significantly associated with an increase in SBP in males and females and with a decrease in level of HDL-C in males only. The change in central pattern of body fat negatively affects the change in established risk factors for cardiovascular diseases early in life.