This study aims to determine prospective effects of the childhood parent-child relationships on the development of cardiovascular risks in adolescence. Using available 917 parent-child dyads from the Study of Early Child Care and Youth Development (1991 to 2006), we analyzed the prospective effects of childhood parent-child relationships of Conflict and Closeness, as well as their categorized combinations (Harmonic, Dramatic, Hostile, and Indifferent) on the development of subscapular and triceps skinfold thickness (SST/TST), body mass index (BMI), systolic and diastolic blood pressure (SBP/DBP), and heart rate (HR) during adolescence. We found that higher levels of Conflict in the relationship with mothers (slope=0.05, P<0.001) and fathers (slope=0.04, P=0.03) increased the growth rate of TST among girls during adolescence, but not among boys. The maternal-girl dyadic with higher Conflict scores also increased girl's growth rate of BMI percentile (slope=0.10, P=0.02), though the paternal-boy dyadic with higher Conflict scores decreased boy's growth rate of BMI percentile (slope=-0.13, P=0.04). A Hostile maternal-son relationship lowered boy's growth rate of SBP (slope=-3.15, P<0.001) and DBP (slope=-4.42, P<0.001). A Dramatic maternal-son relationship increased boy's growth rate of SST (slope=0.89, P<0.001) and TST (slope=0.64, P=0.03). Hostile paternal-daughter relationships were positively associated with the growth rate of TST (slope=0.28, P=0.03). Overall, there was a significant influence of childhood parent-child relationships on the development of cardiovascular risks during adolescence, and the effect was further modified by both parents' and child's gender.