Objectve To study the effect of interaction between ADIPOQ 11377C/G (rs266729) gene polymorphism and physical activity in metabolic syndrome in children. Methods We conducted a case-control study in 114 cases and 114 controls. The genotype of ADIPOQ 11377C/G had been detected in direct sequenc-ing. The effect of interaction between gene polymorphism and physical activity was evaluated by a crossover analysis. Results Efficient physical activity was a protective factor (OR = 0.14); there was interaction between inefficient physical activity and CC genotype of 11377C/G which was a risk factor for metabolic syndrome in children. Conclusion Efficient physical activity can reduce the risk of metabolic syndrome in children. There was interaction between 11377C/G (rs266729) polymorphism and physical activity.