Introduction: The aims of this study were to examine cross-sectional, and longitudinal association of different measures of obesity and physical fitness with cardiovascular disease (CVD) risk factors in adolescents with Down syndrome. Methods: Longitudinal analysis included 90 adolescents with Down syndrome. Obesity and physical fitness were measured following the ALPHA battery. Blood pressure and blood samplings (glucose, total cholesterol, high-density lipoprotein cholesterol, and serum lipid triglycerides levels (mg/dl) were determinated. Results: In cross-sectional analyses, obesity was positively associated with single CVD risk factors and CVD risk factor index (all p < 0.05). In the prospective analyses, obesity was not associated with single CVD risk factors, but components of physical fitness at baseline impact in some single CVD risk factors (all p < 0.05). Conclusion: Obesity might be more strongly related to current cardiovascular-health, while components of physical fitness might be more related to future cardiovascular-health in adolescents with Down syndrome. [This article was written on behalf of the UP&DOWN Study Group.]