In Canada, vaccination policies against the 2009 influenza H1N1 pandemic (H1N1pdm09) were modified at different times during the autumn wave. We hypothesized that ethnicity and place of residence influenced the odds of vaccination. To test this hypothesis, we used vaccination databases for the entire province of Manitoba, and obtained the age distribution of vaccination for First Nations (FN) and non-First Nations (non-FN) populations. We used regression analysis to determine the effect of ethnicity and location of residence on odds of vaccination. We found that individuals with FN identity were over 2.8 times [95% confidence interval (CI) 2.79–2.87] more likely to receive vaccination compared to non-FN individuals. For the FN populations, on-reserve residency was associated with 5.15-fold (95% CI 5.00–5.30) higher odds of vaccination compared to off-reserve residency. Our study highlights the importance of demographic and geographical variables in developing strategies for vaccine prioritization.