While many factors that contribute to the occurrence of lower respiratory tract infections (LRTI) in Canadian indigenous children have been described, the role of aspiration during swallowing has not been explored in these children. Because of an increase in referrals of indigenous children from our catchment area (Manitoba, North Western Ontario, and Nunavut) for assessment of aspiration during swallowing, we retrospectively reviewed the clinical records of 325 consecutive children undergoing videofluoroscopic swallowing studies (VFSS) to evaluate which factors, including indigenous heritage and LRTI, were associated with aspiration during swallowing. Our sample had an overrepresentation of indigenous children (35% compared to 23% in the catchment area). These children were more likely to aspirate during swallowing (P = 0.001) and to have experienced an LRTI prior to the VFSS (P = 0.000). When separating the children who aspirated into two groups based on indigenous heritage, the indigenous children were more likely to have had an LRTI (P = 0.028) than the other children in the sample. With logistic regression analysis, significant correlations between indigenous heritage, LRTI (P = 0.000), and aspiration (P = 0.009) were found. When aspiration during swallowing was the factor of interest, it correlated with both LRTI (P = 0.001) and the presence of congested upper airway noises after eating (P = 0.000). These upper airway noises were strongly associated with aspiration in indigenous children (P = 0.004). While prospective data are required to determine if the correlations seen in this retrospective review will remain robust, indigenous children were more likely to aspirate during swallowing and have LRTI in this sample. Whether aspiration during swallowing is related to environmental, ethnic, or biological factors in indigenous children remains to be determined, but the association between aspiration and congested upper airway noises after eating may assist in the early diagnosis of aspiration during swallowing, and thereby enable timely intervention to decrease aspiration risk in children already at risk of repeated LRTI due to a number of other confounding factors.