To compare the study motives and career choices of senior undergraduate medical and dental students in Iran. A cross-sectional questionnaire-based survey study involving final year medical and dental students from 4 dental and medical schools was conducted in 2010. The questionnaire was designed in three sections (Demographic details, motivational items and career choice items) and after confirming the validity and reliability of the questions, it was distributed among the students. Data were entered into SPSS; statistical analysis included logistic regression and multiple linear regression. The response rate was 62% (n=219) for medical and 64% (n=300) for dental students. The factor analysis identified six motivational items: "Social and professional status", "Health care and people", "Othersʹ recommendation", "personal interest and nature of occupation", "Occupational experience" and "Personal life". Medical students were more influenced by "Playing a role in community health" and "Personal interest". "Work independence" and "Social factors" however were two major influential factors among dental students. There were significant differences in important influences by age (Social and professional status, Othersʹ recommendation), Parentsʹ education (Social and professional status, Health care and people, Personal life) and marital status (single >married: Occupational experience, married > single: Personal life). Engaging in postgraduate studies was the first career preference among 90.9% and 89.8% of dental and medical students respectively. Medical and dental students report a wide range of motivational factors in studying medicine/dentistry and future career plans which is affected by age, parentsʹ education and marital status.