Childhood obesity is a public health problem; in Mexican children a high prevalence of cardiovascular risk factors are present. Physical activity has been proposed as a strategy to reduce this risk. We conducted a pre-posttest intervention study of 214 school-aged Mexican children (4th to 6th grade), to assess the effects of two physical activity routines with different duration and intensity (40 minute aerobic routine vs. 20 minute routine) on cardiovascular risk markers. Physical activity routines were assigned randomly to two public schools in Toluca, Mexico (20 min: group 1 (n= 117), 40 min: group 2 (n=97)). The routines were implemented Monday through Friday for 12 weeks. Nutrition assessment was done before and after the intervention and included anthropometric measurements (weight, height, body mass index, waist circumference and body composition), blood pressure and biochemical analysis (triglycerides, total cholesterol LDL-cholesterol, HDL-Cholesterol, glucose and insulin). Heart rate was monitored 3 times during the intervention to evaluate the routine´s intensity.