Objective: To explore the relationship between migraine and anxiety disorders, mood disorders and perceived mental health in a population-based sample of adolescents. Methods: The Canadian Community Health Survey (CCHS) is a cross-sectional health survey sampling a nationally representative group of Canadians. In this observational study, data on all 61,375 participants aged 12-19 years from six survey cycles were analyzed. The relationships between self-reported migraine, perceived mental health, and mood/anxiety disorders were modeled using univariate and multivariate logistic regression. The migraine–depression association was also explored in a subset of participants using the Composite International Diagnostic Interview–Short Form (CIDI–SF) depression scale. Results: The odds of migraine were higher among those with mood disorders, with the strongest association in 2011-2 (adjusted odds ratio [aOR]=4.59; 95% confidence interval [CI95%]=3.44-6.12), and the weakest in 2009-10 (aOR=3.06, CI95%=2.06-4.55). The migraine–mood disorders association was also significant throughout all cycles, other than 2011-2, when the CIDI–SF depression scale was employed. The odds of migraine were higher among those with anxiety disorders, with the strongest association in 2011-2 (aOR=4.21, CI95%=3.31-5.35) and the weakest in 2010 (aOR=1.87, CI95%=1.10-3.37). The inverse association between high perceived mental health and the odds of migraine was observed in all CCHS cycles, with the strongest association in 2011-2 (aOR=0.58, CI95%=0.48-0.69) and the weakest in 2003-4 (aOR=0.75, CI95%=0.62-0.91). Conclusions: This study provides evidence, derived from a large population-based sample of adolescents, for a link between migraine and mood/anxiety disorders.