Background: Comparisons of birth outcomes between Australian Indigenous and non-Indigenous populations show marked inequalities. These comparisons obscure Indigenous disparities. There is much variation in terms of culture, language, residence, and access to services amongst Australian Indigenous peoples. We examined outcomes by region and remoteness for Indigenous subgroups and explored data for communities to inform health service delivery and interventions.Methods: Our population-based study examined maternal and neonatal outcomes for 7,560 mothers with singleton pregnancies from Australia's Northern Territory Midwives' Data Collection (2003-2005) using uni- and multivariate analyses. Groupings were by Indigenous status; region (Top End (TE)/Central Australia (CA)); Remote/Urban residence; and across two large TE communities.Results: Of the sample, 34.1% were Indigenous women, of whom 65.6% were remote-dwelling versus 6.7% of non-Indigenous women. In comparison to CA Urban mothers: TE Remote (adjusted odds ratio [aOR] 1.47, 95%CI: 1.13, 1.90) and TE Urban mothers (aOR 1.36 (95% CI: 1.02, 1.80) were more likely, but CA Remote mothers (aOR 0.43; 95% CI: 0.31, 0.58) less likely to smoke during pregnancy; CA Remote mothers giving birth at >32 weeks gestation were less likely to have attended ≥ five antenatal visits (aOR 0.55; 95%CI: 0.36, 0.86); TE Remote (aOR 0.71; 95%CI: 0.53, 0.95) and CA Remote women (aOR 0.68; 95%CI: 0.49, 0.95) who experienced labour had lower odds of epidural/spinal/narcotic pain relief; and TE Remote (aOR 0.47; 95%CI: 0.34, 0.66), TE Urban (aOR 0.67; 95%CI: 0.46, 0.96) and CA Remote mothers (aOR 0.52; 95%CI: 0.35, 0.76) all had lower odds of having a 'normal' birth. The aOR for preterm birth for TE Remote newborns was 2.09 (95%CI: 1.20, 3.64) and they weighed 137 g (95%CI: -216 g, -59 g) less than CA Urban babies. There were few significant differences for communities, except for smoking prevalence.Conclusions: This paper is one of few quantifying inequalities between groups of Australian Indigenous women and newborns at a regional level. Indigenous mothers and newborns do worse on some outcomes if they live remotely, especially if they live in the TE. Smoking prevention and high-quality antenatal care is fundamental to addressing many of the adverse outcomes identified in this paper.