Introduction: Pneumonia and diarrhoea are leading causes of death in children. There is a need to develop effective interventions. Objective: We present the design and baseline findings of a community-randomised controlled trial in rural Peru to evaluate the health impact of an Integrated Home-based Intervention Package in children aged 6 to 35. months. Methods: We randomised 51 communities. The intervention was developed through a community-participatory approach prior to the trial. They comprised the construction of improved stoves and kitchen sinks, the promotion of hand washing, and solar drinking water disinfection (SODIS). To reduce the potential impact of non-blinding bias, a psychomotor stimulation intervention was implemented in the control arm. The baseline survey included anthropometric and socio-economic characteristics. In a sub-sample we determined the level of faecal contamination of drinking water, hands and kitchen utensils and the prevalence of diarrhoegenic Escherichia coli in stool specimen. Results: We enrolled 534 children. At baseline all households used open fires and 77% had access to piped water supplies. E. coli was found in drinking water in 68% and 64% of the intervention and control households. Diarrhoegenic E. coli strains were isolated from 45/139 stool samples. The proportion of stunted children was 54%. Conclusions: Randomization resulted in comparable study arms. Recently, several critical reviews raised major concerns on the reliability of open health intervention trials, because of uncertain sustainability and non-blinding bias. In this regard, the presented trial featuring objective outcome measures, a simultaneous intervention in the control communities and a 12-month follow up period will provide valuable evidence. © 2011 Elsevier Inc.