An unresolved question about breastfeeding is its effect on caries, in particular, early childhood caries (ECC). In secondary analyses of data from an ECC intervention, we describe breastfeeding among Aboriginal children and associations between breastfeeding and ECC. Breastfeeding (duration and exclusivity to six months) was grouped into mutually exclusive categories. ECC was observed by a calibrated dental professional. Outcomes were prevalence of ECC (% decayed, missing, and filled teeth in the primary dentition (% dmft>0)) and caries severity (mean number of decayed, missing, and filled surfaces (mean dmfs)) in children aged three years. Analyses were adjusted for confounding. Multiple imputation was undertaken for missing information. Of 307 participants, 29.3% were never breastfed, 17.9% exclusively breastfed to six months, and 9.3% breastfed >24 months. Breastfeeding >24 months was associated with higher caries prevalence (adjusted prevalence ratio (PRa) 2.06 (95%CI 1.35, 3.13, p-value = 0.001) and mean dmfs (5.22 (95% CI 2.06, 8.38, p-value = 0.001), compared with children never breastfed. Exclusive breastfeeding to six months with breastfeeding <24 months was associated with 1.45 higher caries prevalence (95% CI –0.92, 2.30, p-value = 0.114) and mean dmfs 2.04 (−0.62, 4.71, p-value = 0.132), compared with never breastfeeding. The findings are similar to observational studies on breastfeeding and caries but not with randomized controlled trials of breastfeeding interventions. Despite attending to potential biases, inconsistencies with trial evidence raises concerns about the ability to identify causal effects of breastfeeding in observational research.