Objective: The aim of the present study was to investigate secular trends in selected cardiovascular disease risk factors (namely adiposity, physical activity, physical fitness and diet) in a sample of Welsh 12-13 year olds between 2002 and 2007. Design: Cross-sectional. Setting: A secondary school based in South West Wales. Method: Two studies in 2002 (n = 71) and 2007 (n = 83), were compared to evaluate changes in adiposity, physical activity, physical fitness and diet in school children. On both occasions testing was carried out in the same school and using identical procedures. Results: Between the two time periods, mean adiposity levels remained stable. The percentage of school children who were classified as overweight or obese in 2002 was 39.4 per cent (boys) and 26.3 per cent (girls). In 2007, this was 21.3 per cent and 26.0 per cent respectively. Physical activity and fitness levels improved for boys and girls; however, 80.0 per cent of girls still did not meet the recommended one hour per day of moderate physical activity. For both sexes, there were no significant differences in dietary fat intake between 2002 and 2007 cohorts. Both boys and girls continued to consume a diet that was heavily reliant on foods that were high in saturated fat. Conclusion: We identified a trend towards increased physical activity among 12-13 year olds but there were no changes in dietary habits or adiposity. The findings indicate that increased physical activity, used in isolation without dietary modification, has no effect on adiposity. This study has demonstrated a need for large-scale studies to better evaluate existing and future initiatives targeting obesity in young people. (Contains 3 tables.)