As part of an international project on the impact of colonisation on Indigenous populations, we use data from the Koori Health Research Database (KHRD) to outline the demographic, epidemiological and health transitions of the Victorian Koori population from colonisation through to the resurgence of population in the twentieth century. We examine issues of population definition, and present new fertility and survival analysis for the Koori population. We demonstrate that the health transition of the Koori population under colonisation differs radically from the transitions in national populations in the course of modernisation.