This study aimed to investigate an interaction between energy intake, physical activity, and UCP2 gene variation on weight gain and adiposity changes in Indonesian adults. This is a prospective cohort study conducted in 323 healthy adults living in the city of Yogyakarta, Indonesia. Energy intake, physical activity, body weight, body mass index (BMI), percent body fat, waist to hip ratio (WHR) were measured at baseline and after two years while and UCP2 -866G/A gene variation was determined at baseline. We reported that after two years subjects had a significant increment in body weight, BMI, body fat and reduction in WHR (all p<0.05). In all subjects, total energy intake was significantly correlated with changes in body weight (B=0.128, p=0.023) and body fat (B=0.123, p=0.030). Among subjects with GG genotype, changes in energy intake was positively correlated with changes in body weight (B=0.232, p=0.016) and body fat (B=0.201, p=0.034). These correlations were insignificant among those with AA+GA genotypes (all p>0.05). In summary, we show that UCP2 gene variation might influence the adiposity response towards changes in energy intake. Subjects with GG genotype of UCP2 -866G/A gene were more responsive to energy intake thus more prone to weight gain due to overeating.