Objective: The aim of this study was to evaluate the prevalence of psychiatric morbidity, alcohol use, burnout and compassion satisfaction among physician trainees in New South Wales, Australia, and examine links between personal, demographic and lifestyle factors. Methods: A total of 67 physician trainees were recruited to the study. Fifty-nine completed the online survey (88% response rate). Outcome measures included the Depression Anxiety Stress Scale, Professional Quality of Life Scale and Alcohol Use Disorders Identification Test. Results: Approximately half the respondents met screening criteria for depression (53%), stress (51%) and anxiety (46%). Secondary traumatic stress was exceptionally high across the cohort, with higher scores in females (P = 0.001). The main reasons for not seeking help for depression or anxiety were lack of time (81%), fear of lack of confidentiality or privacy (41%), embarrassment (39%) and effect on registration (27%). Eighty-eight per cent of respondents agreed that doctors feel they need to portray a healthy image, but only 54% engaged in regular exercise and 24% slept ≤6 h each day. Conclusion: The results demonstrate high levels of non-psychotic psychiatric morbidity among physician trainees and a need to improve their well-being. Workplace systems need to promote healthy work environments and support physician trainees through good mentorship and supervision. What is known about the topic?: Doctors' health and patient care can be affected when doctors experience burnout and psychiatric morbidity. What does this paper add?: This paper adds to the evidence of psychiatric morbidity, burnout, secondary trauma and increased demographic data on a cohort of junior doctors undertaking speciality training. In addition, it provides reasons for not seeking help and positive and negative coping methods used by these junior doctors. What are the implications for practitioners?: The level of distress is high and requires system changes to support both individual health measures and structural change to work and study programs.