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Abstract Background Given the looming shortage of physicians in Canada, we wished to determine how closely the career preference of students entering Canadian medical schools was aligned with the current physician mix in Canada. Methods Career choice information was collected from a survey of 2,896 Canadian medical students upon their entry to medical school. The distribution of career choices of survey respondents was compared to the current physician speciality mix in Canada. Results We show that there is a clear mismatch between student career choice at medical school entry and the current specialty mix of physicians in Canada. This mismatch is greatest in Urban Family Medicine with far fewer students interested in this career at medical school entry compared to the current proportion of practicing physicians. There are also fewer students interested in Psychiatry than the current proportion of practicing physicians. Conclusion This mismatch between the student interest and the current proportion of practicing physicians in the various specialities in Canada is particularly disturbing in the face of the current sub-optimal distribution of physicians. If nothing is done to correct this mismatch of student interest in certain specialities, shortages and misdistributions of physicians will be further amplified. Studies such as this can give a window into the future health human resources challenges for a nation.