Background: Research literature consistently documents that scientifically based therapeutic recommendations are not always followed in the hospital or in the primary care setting. Currently, there is evidence that some general practitioners in Australia are not prescribing appropriately for patients diagnosed with 1) hypertension (HT) and 2) chronic heart failure (CHF). The objectives of this study were to improve general practitioners drug treatment management of these patients through feedback on their own prescribing and small group discussions with peers and a trained group facilitator. The impact evaluation includes quantitative assessment of prescribing changes at 6, 9, 12 and 18months after the intervention. Methods. A pragmatic multi site cluster RCT began recruiting practices in October 2009 to evaluate the effects of a multi-faceted quality improvement (QI) intervention on prescribing practice among Australian general practitioners (GP) in relation to patients with CHF and HT. General practices were recruited nationally through General Practice Networks across Australia. Participating practices were randomly allocated to one of three groups: two groups received the QI intervention (the prescribing indicator feedback reports and small group discussion) with each group undertaking the clinical topics (CHF and HT) in reverse order to the other. The third group was waitlisted to receive the intervention 6months later and acted as a control for the other two groups.De-identified data on practice, doctor and patient characteristics and their treatment for CHF and HT are extracted at six-monthly intervals before and after the intervention. Post-test comparisons will be conducted between the intervention and control arms using intention to treat analysis and models that account for clustering of practices in a Network and clustering of patients within practices and GPs. Discussion. This paper describes the study protocol for a project that will contribute to the development of acceptable and sustainable methods to promote QI activities within routine general practice, enhance prescribing practices and improve patient outcomes in the context of CHF and HT. Trial registration: Australian New Zealand Clinical Trials Registry (ANZCTR), Trial # 320870.