Obesity in childhood is increasing worldwide. To combat overweight and obesity in childhood, the school-based Children’s Health InterventionaL Trial (CHILT) project combines health education and physical activity. This paper examines the effect of intervention on the body mass index (BMI) and motor abilities after 20.8 ± 1.0 months in 12 randomly selected primary schools compared with 5 randomly selected control schools. The anthropometric data were assessed, BMI was calculated. Coordination was determined by lateral jumping and endurance performance by a 6-minute run. No difference in the prevalence of overweight and obesity was found between the intervention (IS) and control schools (CS) either at baseline or following intervention (each p > 0.05). The increase in the number of lateral jumps was significantly higher in the IS than in the CS (p < 0.001). For the 6-minute run the increase in distance run was significantly improved in IS (p = 0.020). All variables were controlled for gender and age. Overweight and obese children in both IS and CS produced significantly lower scores in coordination and endurance tasks than normal and underweight children during both examinations (each p ≤ 0.001), adjusted for gender and age. Preventive intervention in primary schools offers an effective means to improve motor skills in childhood and to break through the vicious circle of physical inactivity - motor deficits - frustration - increasing inactivity possibly combined with an excess energy intake and weight gain. To prevent overweight and obesity these measures have to be intensified.