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Early identification of vulnerable children to protect them from harm and support them in achieving their long-term potential is a community priority. This is particularly important in the Northern Territory (NT) of Australia, where Aboriginal children are about 40% of all children, and for whom the trauma and disadvantage experienced by Aboriginal Australians has ongoing intergenerational impacts. Given that shared social determinants influence child outcomes across the domains of health, education and welfare, there is growing interest in collaborative interventions that simultaneously respond to outcomes in all domains. There is increasing recognition that many children receive services from multiple NT government agencies, however there is limited understanding of the pattern and scale of overlap of these services. In this paper, NT health, education, child protection and perinatal datasets have been linked for the first time. The records of 8,267 children born in the NT in 2006–2009 were analysed using a person-centred analytic approach. Unsupervised machine learning techniques were used to discover clusters of NT children who experience different patterns of risk. Modelling revealed four or five distinct clusters including a cluster of children who are predominantly ill and experience some neglect, a cluster who predominantly experience abuse and a cluster who predominantly experience neglect. These three, high risk clusters all have low school attendance and together comprise 10–15% of the population. There is a large group of thriving children, with low health needs, high school attendance and low CPS contact. Finally, an unexpected cluster is a modestly sized group of non-attendees, mostly Aboriginal children, who have low school attendance but are otherwise thriving. The high risk groups experience vulnerability in all three domains of health, education and child protection, supporting the need for a flexible, rather than strictly differentiated response. Interagency cooperation would be valuable to provide a suitably collective and coordinated response for the most vulnerable children.