BACKGROUND: The purpose of this study was to examine the physiological, anthropometric and motor development characteristics of rural children between the ages of 5-7 years old in Nkonkobe Municipality, South Africa. METHODS: The study involved 305 school children (159 boys and 146 girls) randomly selected from primary schools in Alice sub-district, Nkonkobe Municipality. Body weight, height, skinfold thickness and girth measurements were measured using standard procedures. Overweight and obesity were defined using Body Mass Index (BMI) for age and gender. Motor development was assessed using Test of Gross Motor Development (TGMD-2). RESULTS: The proportion of overweight was 15.8% and 10.7% for girls and boys, respectively. Obesity was higher among the boys (16.4%) compared to girls (10.3%). Girls performed better (40.9 +/- 6.54) than boys (39.7 +/- 6.64) in locomotor skills test. Conversely, boys performed better (39.8 +/- 7.62) than girls (38.6 +/- 7.29) in object control. CONCLUSIONS: The prevalence of overweight and obesity among the children is high and concerning for their health. At all ages, girls had higher body fat percentage and fat mass compared to the boys. The locomotor raw score was higher in girls than in boys, while the object control raw score was higher in boys compared to girls. The non-correlation of BMI with TGMD-2 tests suggests an equal potential of motor development among the children, regardless of their body fatness. There is need for obesity prevention program in schools, and the promotion of physical activity in children.