Stigmatisation towards depression has previously been reported amongst medical students from a variety of backgrounds. This study explored personal and perceived stigmas associated with depression, and their relationship with demographics, knowledge of depression, levels of personal stress and history of medical illness amongst Australian-trained medical students. A cross-sectional survey was undertaken amongst students enroled June-to-August 2009 across four Australian medical schools. In total, 1010 students completed the survey, a response rate of 29.6%. Approximately 25% of students reported a past history of depression. Higher stress (K-10 scores) was reported by females and those with a past history of depression. On a scale of 0-to-5, the mean (±S.D.) personal and perceived stigma depression scores were 1.83±1.49 and 4.05±1.42 respectively. In multivariate analysis, higher perceived stigma and K-10 scores, a past history of anxiety and Year 3 of medical school indicated higher personal stigma scores. Perceived stigma was positively associated with K-10 scores, personal stigma scores, and a Caucasian background. Our findings suggest a high level of personal and particularly perceived stigma associated with depression amongst medical students, especially those displaying higher levels of stress. Adequate support and screening for psychological stress may de-stigmatise depression and improve mental health amongst future Australian doctors.