Objective: This study aimed to evaluate the effectiveness of the Making the Difference programme (MTDP), an education-and activity-based intervention for Grade 4 learners at primary schools in the Western Cape. Design: This was a cross-sectional, post-intervention survey of an existing programme, using control schools as a comparator. Setting and subjects: The study involved Western Cape primary schools in the 2009 school year. Schools were randomly sampled from two regions. Four intervention (active in the MTDP) and five control (non-participating) schools (n = 325 learners) were selected. Outcome measures: The following outcome measures were assessed using an administered questionnaire to learners: learners' knowledge of, attitudes towards, and behaviour in relation to nutrition and physical activity. Results: A small but significant improvement (eating vegetables and taking lunch boxes to school) was demonstrated with regard to self-reported behaviour in relation to nutrition in the intervention group. However, this behaviour was not explained by differences in barriers to healthy eating, self-efficacy or knowledge, which were not different between the groups, or by perceived social support, which was actually significantly increased in the control group. Groups displayed no differences in physical activity or sedentary behaviour. However, the results showed a significant difference between the groups in terms of a reduction in perceived barriers to physical activity and increased physical activity self-efficacy in the active group. Conclusion: While the MTDP only had a modest effect on the self-reported nutrition and physical activity behaviour of the learners, results regarding lower perceived barriers to physical activity and increased physical activity self-efficacy were promising