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Background: Childhood obesity is a serious public health challenge and schools have been identified as an ideal place to implement prevention interventions. The aim of this study was to measure the cost-effectiveness of a multi-faceted school-based obesity prevention intervention targeting children aged 6–7 years when compared to ‘usual activities’. Methods: A cluster randomised controlled trial in 54 schools across the West Midlands (UK) was conducted. The 12-month intervention aimed to increase physical activity by 30 minutes per day and encourage healthy eating. Costs were captured from a public sector perspective and utility-based health related outcomes measured using the CHU-9D. Multiple imputation using chained equations was used to address missing data. The cost effectiveness was measured at 30 months from baseline using a hierarchical net-benefit regression framework, that controlled for clustering and prespecified covariates. Any uncertainty in the results was characterised using cost-effectiveness acceptability curves. Results: At 30 months, the total adjusted incremental mean cost of the intervention was £155 (95% confidence interval [CI]: £139, £171), and the incremental mean QALYs gained was 0.006 (95% CI: -0.024, 0.036), per child. The incremental cost-effectiveness at 30 months was £26,815 per QALY and using a standard willingness to pay threshold of £30,000 per QALY, there was a 52% chance that the intervention was cost-effective. Conclusions: The cost-effectiveness of the school-based WAVES intervention was subject to substantial uncertainty. We therefore recommend more research to explore obesity prevention within schools as part of a wider systems approach to obesity prevention. Trial registration: This paper uses data collected by the WAVES trial: Controlled trials (registered May 2010). [ABSTRACT FROM AUTHOR]