BackgroundThe environment for medical education in Iraq has been difficult for many years. The 2003 invasion of Iraq accelerated a steady emigration of faculty and graduates. Kidnappings and deaths of doctors became commonplace. To understand current career plans, expectations and perceptions of medical students, three Baghdad medical schools were surveyed.MethodsWritten questionnaires were completed by 418 medical students variously in their 4th, 5th and 6th (final)years of training. We asked about perceptions of the quality of their medical education, the quality of health services in Iraq generally, and about deaths, injuries and migration of faculty, classmates and family.ResultsThe average age of students was 22 years, with 59% women. Most students (90%) were originally from Baghdad. Although there were some positive responses, many students (59%) rated the overall quality of their medical education as fair or poor. Three-fourths of students believed the quality of hospital care in Iraq to be only fair or poor. A majority of students (57%) stated they were thinking frequently or all the time about leaving Iraq after graduation. Reasons given for leaving included the desire for further education, seeking a better lifestyle and fleeing conflict. Leading reasons for staying included the pull of friends and family, familiarity with the health system, and a sense of responsibility to the country. Nearly one in five (18%) students reported the death of a family member attributable to intentional violence, and 15% reported the violent death of a medical school classmate or faculty member since the 2003 invasion. Half the students reported at least one school faculty members had left Iraq because of the war.ConclusionMedical students hold a mediocre view of the quality of their medical education and of Iraq’s health system. Many of their faculty members have left the country. The majority of students may leave Iraq after graduation, afforded the opportunity. This poses a significant problem for staffing an already demoralized and stressed health system. Current circumstances suggest the situation will continue to deteriorate.Electronic supplementary materialThe online version of this article (10.1186/s12909-018-1156-8) contains supplementary material, which is available to authorized users.