Objective: The aim of the present study was to review the methodological literature regarding evaluation methods for complex public health interventions broadly and, based on such methods, to critically reflect on the evaluation of contemporary community-based obesity prevention programmes. Design: A systematic review of the methods and community-based literature was performed by one reviewer. Results: The review identified that there is considerable scope to improve the rigour of community-based obesity prevention programmes through: prospective trial registration; the use of more rigorous research designs, particularly where routine databases including an objective measure of adiposity are available; implementing strategies to quantify and reduce the risk of selective non-participation bias; the development and use of validated instruments to assess intervention impacts; reporting of intervention process and context information; and more comprehensive analyses of trial outcomes. Conclusions: To maximise the quality and utility of community-based obesity prevention evaluations, programme implementers and evaluators need to carefully examine the strengths and pitfalls of evaluation decisions and seek to maximise evaluation rigour in the context of political, resource and practical constraints.