Background and objective: Primary hypertension in children is becoming a global threat for the growing economic burden of hypertension management in adulthood and sustainable healthcare. We determined the associations of adolescent blood pressure (BP) with target organ damage markers (carotid intima-media thickness (CIMT) and left ventricular mass index (ilVM)) over a four year period, stratified by childhood BP status at baseline. Methods: We included 421 Black and 307 White South African adolescents (mean age: 11.04 years) with complete follow-up data for BP, CIMT and iLVM. Standard anthropometric measures and basic demographic information were collected. Results: Children were stratified by baseline BP status, i.e., normotensive; n=454 (57.5% Black and 57.7% female) and elevated BP; n=274 (58.4% Black and 52.2% female), with comparable proportions of ethnicity (p=0.81) and sex (p=0.15). Systolic BP (by 6mmHg; p<0.001), diastolic BP (by 3mmHg; p<0.001) and perfusion pressure (by 4mmHg; p<0.001) as well as sex-specific body mass index for age z-scores (BAZ; p<0.001) were all higher in the elevated BP compared to normotensive group. Groups were comparable for age (p=0.78), CIMT (p=0.28) and iLVM (p=0.64). In partial regression analysis (adjusting for ethnicity, sex, follow-up age and BAZ), systolic BP correlated positively with CIMT (r=0.125; p=0.041) and iLVM (r=0.184; p=0.002) in the elevated BP group only. Backward multiple adjusted linear regression analysis (adjustment for perfusion pressure at baseline, age, sex, ethnicity and BAZ) showed adverse associations of systolic BP with CIMT (β=0.126; p=0.046) and iLVM (β=0.199; p=0.001), and diastolic BP with iLVM (β=0.130; p=0.002), only in children with elevated BP at baseline. Conclusion: Elevated BP in early childhood contributes to the long-term impact on target organ health during adolescence independent of sex and ethnicity, while the association of BP with iLVM seems to be moderated by excess adiposity.