BACKGROUND Despite there being considerable literature documenting learner distress and perceptions of mistreatment in medical education settings, these concerns have not been explored in-depth in Canadian family medicine residency programs. The purpose of the study was to examine intimidation, harassment and/or discrimination (IHD) as reported by Alberta family medicine graduates during their two-year residency program. METHODS A retrospective questionnaire survey was conducted of all (n = 377) family medicine graduates from the University of Alberta and University of Calgary who completed residency training during 2001-2005. The frequency, type, source, and perceived basis of IHD were examined by gender, age, and Canadian vs international medical graduate. Descriptive data analysis (frequency, crosstabs), Chi-square, Fisher's Exact test, analysis of variance, and logistic regression were used as appropriate. RESULTS Of 377 graduates, 242 (64.2%) responded to the survey, with 44.7% reporting they had experienced IHD while a resident. The most frequent type of IHD experienced was in the form of inappropriate verbal comments (94.3%), followed by work as punishment (27.6%). The main sources of IHD were specialist physicians (77.1%), hospital nurses (54.3%), specialty residents (45.7%), and patients (35.2%). The primary basis for IHD was perceived to be gender (26.7%), followed by ethnicity (16.2%), and culture (9.5%). A significantly greater proportion of males (38.6%) than females (20.0%) experienced IHD in the form of work as punishment. While a similar proportion of Canadian (46.1%) and international medical graduates (IMGs) (41.0%) experienced IHD, a significantly greater proportion of IMGs perceived ethnicity, culture, or language to be the basis of IHD. CONCLUSIONS Perceptions of IHD are prevalent among family medicine graduates. Residency programs should explicitly recognize and robustly address all IHD concerns.