A recent study of the health of Indigenous children in four First Nations Communities in remote northwestern Ontario found that 21% of children had been admitted to hospital for respiratory infections before age 2 years. Here we report a detailed analysis of the housing conditions in these communities. We employed a variety of statistical methods, including linear regression, mixed models, and logistic regression, to assess the correlations between housing conditions and loadings of biocontaminants (dust mite allergens, fungal glucan, and endotoxin) and indoor concentrations of PM2.5, CO2, benzene, and formaldehyde. The houses (n = 101) were crowded with an average of approximately 7 people. Approximately 27% of the homes had sustained CO2 concentrations above 1500 ppm. Most homes had more than one smoker. Commercial tobacco smoking and the use of non-electric heating (e.g., wood, oil) were associated with increased fine particle concentrations. Over 90% of the homes lacked working Heat Recovery Ventilators (HRVs), which was associated with increased fine particle concentrations and higher CO2. Of the 101 homes, 12 had mold damage sufficient to increase the relative risk of respiratory disease. This resulted from roof leaks, through walls or around the windows due to construction defects or lack of maintenance. A similar percentage had mold resulting from condensation on windows. Endotoxin loadings were much higher than any previous study in Canada. This work provides evidence for the need for more effort to repair existing houses and to ensure the HRVs are properly installed and maintained.