The cluster randomized trial (CRT) is used increasingly in knowledge translation research, quality improvement research, community based intervention studies, public health research, and research in developing countries. However, cluster trials raise difficult ethical issues that challenge researchers, research ethics committees, regulators, and sponsors as they seek to fulfill responsibly their respective roles. Our project will provide a systematic analysis of the ethics of cluster trials. Here we have outlined a series of six areas of inquiry that must be addressed if the cluster trial is to be set on a firm ethical foundation: 1. Who is a research subject? 2. From whom, how, and when must informed consent be obtained? 3. Does clinical equipoise apply to CRTs? 4. How do we determine if the benefits outweigh the risks of CRTs? 5. How ought vulnerable groups be protected in CRTs? 6. Who are gatekeepers and what are their responsibilities? Subsequent papers in this series will address each of these areas, clarifying the ethical issues at stake and, where possible, arguing for a preferred solution. Our hope is that these papers will serve as the basis for the creation of international ethical guidelines for the design and conduct of cluster randomized trials.