BACKGROUND Streptococcus pneumoniae, Moraxella catarrhalis, and nontypeable Haemophilus influenzae is associated with otitis media (OM). Data are limited on risk factors for carriage of these pathogens, particularly for Indigenous populations. We investigated predictors of nasopharyngeal carriage in Australian Aboriginal and non-Aboriginal children. METHODS Nasopharyngeal aspirates were collected up to 7 times before age 2 years from 100 Aboriginal and 180 non-Aboriginal children. Longitudinal modeling estimated effects of environmental factors and concurrent carriage of other bacteria on the probability of bacterial carriage. We present a novel method combining the effects of number of household members and size of house into an overall crowding model. RESULTS Each additional household member increased the risk of carriage of S. pneumoniae (odds ratio [OR] = 1.45 per additional Aboriginal child in a 4-room house, 95% confidence interval [CI]: 1.15-1.84; OR = 2.34 per additional non-Aboriginal child, 95% CI: 1.76-3.10), with similar effect sizes for M. catarrhalis, and nontypeable Haemophilus influenzae. However, living in a larger house attenuated this effect among Aboriginal children. Daycare attendance predicted carriage of the 3 OM-associated bacteria among non-Aboriginal children. Exclusive breast-feeding at 6 to 8 weeks protected against Streptococcus aureus carriage (OR = 0.42, 95% CI: 0.19-0.90 in Aboriginal children and OR = 0.49, 95% CI: 0.25-0.96 in non-Aboriginal children). OM-associated bacteria were more likely to be present if there was concurrent carriage of the other OM-associated species. CONCLUSIONS This study highlights the importance of household transmission in carriage of OM bacteria, underscoring the need to reduce the crowding in Aboriginal households.