Redressing developmental and school learning inequalities among children requires an understanding of the factors that influence development across population groups. This study utilized the 2009 Australian Early Development Census (AEDC) to explore the association of perinatal health and socio-demographic factors with early development of children in the Northern Territory of Australia. The study cohort included 1110 Aboriginal and 812 non-Aboriginal children, most aged 5 years, whose developmental status was assessed during their first year of full-time school enrollment. Individual-level information was probabilistically linked across three administrative datasets. Logistic regression models were used to estimate the association (odds ratio (OR)) between early life characteristics of children and teacher-rated vulnerability on one or more of five domains of development. The crude OR for developmental vulnerability was much greater for Aboriginal than non-Aboriginal children (OR: 6.93, 95% CI: 5.62-8.56). After adjustment for other variables, the increased risk of developmental vulnerability for Aboriginal children was substantially moderated (OR: 1.68, 95% CI: 1.21-2.32). Influential factors in the adjusted model included: English as a second language (OR: 3.11, 95% CI: 2.27-4.26), gestational age at birth of 34-36 weeks (OR: 2.08, 95% CI: 1.27-3.39) and living in a very remote area (OR: 1.68, 95% CI: 1.19-2.37). There was a gradient in the strength of the association with the level of primary caregiver's education. An additional risk, for Aboriginal children only, was not having attended a day care or pre-school program (OR: 1.43, 95% CI: 1.01-2.04). The study demonstrates the emerging capacity for linkage of data across administrative datasets to inform our understanding of the extent to which multiple factors in early-life operate in their association with children's early development. Our findings are of particular relevance to initiatives to improve outcomes for Aboriginal children by demonstrating that potentially modifiable health and socio-economic factors account for almost all of the difference in developmental vulnerabilities observed between Aboriginal and non-Aboriginal children.