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INTRODUCTION We examined the concordance between the Canadian Community Health Survey (CCHS) “identity” and “ancestry” questions used to estimate the size of the Aboriginal population in Canada and whether the different definitions affect the prevalence of selected chronic diseases. METHODS Based on responses to the “identity” and “ancestry” questions in the CCHS combined 2009-2010 microdata file, Aboriginal participants were divided into 4 groups: (A) identity only; (B) ancestry only; (C) either ancestry or identity; and (D) both ancestry and identity. Prevalence of diabetes, arthritis and hypertension was estimated based on participants reporting that a health professional had told them that they have the condition(s). RESULTS Of participants who identified themselves as Aboriginal, only 63% reported having an Aboriginal ancestor; of those who claimed Aboriginal ancestry, only 57% identified themselves as Aboriginal. The lack of concordance also differs according to whether the individual was First Nation, Métis or Inuit. The different method of estimating the Aboriginal population, however, does not significantly affect the prevalence of the three selected chronic diseases. CONCLUSION The lack of concordance requires further investigation by combining more cycles of CCHS to compare discrepancy across regions, genders and socio-economic status. Its impact on a broader list of health conditions should be examined.