ObjectiveTo assess whether estimates of survey structured interview diagnoses of mood and anxiety disorders were concordant with diagnoses of these disorders obtained from health administrative data.MethodsAll Ontario respondents to the 2012 Canadian Community Health Survey‐Mental Health (CCHS‐MH) were linked to health administrative databases at ICES (formerly known as the Institute for Clinical Evaluative Sciences). Survey structured interview diagnoses were compared with health administrative data diagnoses obtained using a standardized algorithm. We used modified Poisson regression analyses to assess whether socio‐demographic factors were associated with concordance between the two measures.ResultsOf the 4157 Ontarians included in our sample, 20.4% had either a structured interview diagnosis (13.9%) or health administrative diagnosis (10.4%) of a mood or anxiety disorder. There was high discordance between measures, with only 19.4% agreement. Migrant status, age, employment, and income were associated with discordance between measures.ConclusionsOur findings indicate that previous estimates of the 12‐month prevalence of mood and anxiety disorders in Ontario may be underestimating the true prevalence, and that population‐based surveys and health administrative data may be capturing different groups of people. Understanding the limitations of data commonly used in epidemiologic studies is a key foundation for improving population‐based estimates of mental disorders.