Through-school nutrition and physical activity interventions are designed to help reduce excess weight gain and risk of chronic disease. From 2004 to 2006, Project Energize was delivered in the Waikato Region of New Zealand as a longitudinal randomised controlled study of 124 schools (year 1-6), stratified by rurality and social deprivation, and randomly assigned to intervention or control. Children (686 boys and 662 girls) aged 5 (1926) and 10 (1426) years (692 interventions and 660 controls) had height, weight, body fat (by bioimpedance) and resting blood pressure (BP) measured at baseline and 2 years later. Each intervention school was assigned an 'Energizer'; a trained physical activity and nutrition change agent, who worked with the school to achieve goals based on healthier eating and quality physical activity. After adjustment for baseline measures, rurality and social deprivation, the intervention was associated with a reduced accumulation of body fat in younger children and a reduced rate of rise in systolic BP in older children. There was some evidence that the pattern of change within an age group varied with rurality, ethnicity and sex. We conclude that the introduction of an 'Energizer led' through-school programme may be associated with health benefits over 2 years, but the trajectory of this change needs to be measured over a longer period. Attention should also be paid to the differing response by ethnicity, sex, age group and the effect of rurality and social deprivation.