Introduction: In Chile there are no studies regarding the effects of physical activity on nutritional status of children with Down Syndrome. Objective: To evaluate the impact of a 12 week physical education program on the nutritional status, aerobic capacity and muscle strength in children with Down Syndrome. Subjects and Methods: Between August and November of 2006, a group of 18 children (10 males and 8 females) with Down Syndrome, aged between 5-9 years, underwent to a physical activity program over a 12 week period. A diagnostic and final evaluation of muscle strength variables (dorsal, abdominal and quadriceps) and aerobic capacity was done. Nutritional status was assessed by P/E and T/E (Fundación Catalana), IMC, IP/T and percentage of body fat. Results: Significant differences in muscle strength, aerobic capacity, IP/T and waist circumference were observed between the pre-test and post-test (p < 0.05). At the beginning of the intervention, 53% were overweight according to IMC, 26% to P/E and 68% according to IP/T; with an average percentage of body fat of 22.6%. Conclusion: Although the period of intervention was brief, a significant improvement was noted in muscle strength, aerobic capacity, IP/T and waist circumference. According to our results, there is a high prevalence of overweight status and obesity in this population of children with DS in which intervention with adequate physical activity is vital.