Introduction: The Pro12Ala variant of the Peroxisome Proliferator Activated Receptor Gamma (PPARγ) is one of the critical genetic factor predispose to positive energy balance leading to obesity. Objective: This study aimed to determine the association between Pro12Ala variant in the PPARγ gene with body mass index (BMI) status, physical activity and fat intake among Malay children. Methods: A total of 119 participants aged between 9-11 years old from primary schools in Kota Bharu, Kelantan were recruited. Anthropometric measurements were taken and activity counts of the participants were recorded using accelerometer (Actigraph GT3X+). A food diary was distributed to all participants to collect the data of their fat intake. Genotyping was performed using High Resolution Melting (HRM) analysis. Data obtained were analysed using SPSS version 19. Results: There was a significant association between Pro12Ala variant in the PPARγ gene with BMI status. The allelic frequency of wildtype (Ala/ala) and heterozygous (Pro/ala) among overweight group were 0.83 and 0.17 respectively and 0.92 and 0.08 in the normal weight group (p=0.03). There was a significant difference in BMI, waist circumference and hip circumference between heterozygous and wildtype groups. Conclusion: The study found that there was a significant role of Pro12Ala variant in the PPARγ gene in overweight Malay children.