Short-term humanitarian medical volunteerism has grown significantly among both clinicians and trainees over the past several years. Increasingly, both volunteers and their respective institutions have faced important challenges in regard to medical ethics and professional codes that should not be overlooked. We explore these potential concerns and their risk factors in three categories: ethical responsibilities in patient care, professional responsibility to communities and populations, and institutional responsibilities towards trainees. We discuss factors increasing the risk of harm to patients and communities, including inadequate preparation, the use of advanced technology and the translation of Western medicine, issues with clinical epidemiology and test utility, difficulties with the principles of justice and clinical justice, the lack of population-based medicine, sociopolitical effects of foreign aid, volunteer stress management, and need for sufficient trainee supervision. We review existing resources and offer suggestions for future skill-based training, organisational responsibilities, and ethical preparation.