Human rights and ethical principles justify Indigenous control of health research conducted in Indigenous communities, but also emphasise the need for scientific rigour, knowledge and expertise, much of which currently resides with the non-Indigenous community. In 1994, we began development of the Bibbulung Gnarneep Project on Aboriginal maternal and child health in Perth, Western Australia. We describe the process of developing a protocol to ensure ethical conduct of this research through consultation and negotiation between Aboriginal and non-Aboriginal people involved in the project.