Adolescent obesity has increased dramatically in several countries in recent decades; however, the contribution of physical activity level to adolescent adiposity requires clarification. This article investigates the effect of physical activity on subsequent levels of adiposity in adolescence. The methodological aspects of the studies included in this article, particularly in terms of measurement accuracy for both exposure (physical activity) and outcome (adiposity) variables, are also evaluated. Systematic searches of the literature were undertaken using online databases, including PubMed/MEDLINE, examination of citations and contacting of authors. The online databases were searched from their earliest records until 2007. Only longitudinal studies with 50 or more adolescents were included. Two independent reviewers assessed the quality of the studies using the Downs and Black checklist. Thirteen observational, five experimental and six quasi-experimental studies (without a control group) were identified. Almost all studies were carried out in high-income settings and showed protective effects of physical activity for both prevention and treatment of adolescent obesity. However, experimental studies undertaken with obese adolescents at baseline usually combined physical activity with dietary changes, making it difficult to assess the effect of physical activity itself on the treatment of obesity. Physical activity estimated from questionnaires and body mass index (BMI) were the most frequently used measures. Despite the feasibility of using these approaches in epidemiological studies, significant limitations are evident. Questionnaires are subjective and adolescents may not report physical activity level accurately. Furthermore, BMI is not an accurate measure of fatness for adolescents, as it is also associated with lean mass, hence bias may arise from its longitudinal association with physical activity level. Despite the majority of studies reviewed showing protective effects of physical activity on adiposity, particularly in individuals who are obese at baseline, the current literature on this issue is sparse and several methodological drawbacks are evident. The main limitations relate to a lack of validity in the measurements of both physical activity and body composition. Further studies are needed in order to generate evidence-based recommendations for the quantity and quality of adolescent physical activity required to prevent or treat adolescent obesity.