BACKGROUND: Obesity and lack of physical activity are fast becoming a concern among Malaysian adolescents. OBJECTIVE: This study aims to assess physical activity levels among Malaysian adolescents and investigate the association between physical activity levels and body composition such as body mass index (BMI), waist circumference (WC) and percentage of body fat. SUBJECTS AND METHODS: 1361 school-going 13 year old multi-ethnic adolescents from population representative samples in Malaysia were involved in our study. Self-reported physical activity levels were assessed using the validated Malay version of the Physical Activity Questionnaire for Older Children (PAQ-C). Height, weight, body fat composition and waist circumference (WC) were measured. Data collection period was from March to May 2012. RESULTS: 10.8% of the males and 7.4% of the females were obese according to the International Obesity Task Force standards. A majority of the adolescents (63.9%) were physically inactive. There is a weak but significant correlation between physical activity scores and the indicators of obesity. The adjusted coefficient for body fatness was relatively more closely correlated to physical activity scores followed by waist circumference and lastly BMI. CONCLUSION: This study demonstrates that high physical activity scores were associated with the decreased precursor risk factors of obesity.