Background: Female students currently outnumber male students in most medical schools. Some medical specialties are highly gender segregated. Therefore, it is interesting to know whether medical students have early specialization preferences based on their gender. Consequently, we like to know importance stipulated to motivational factors. Aim: Our study investigates new medical students' early specialization preferences and motivational factors. Methods: New students at a Dutch medical school (n = 657) filled in a questionnaire about specialty preferences (response rate = 94%; 69.5% female, 30.5% male). The students chose out of internal medicine, psychiatry, neurology, pediatrics, surgery, gynecology and family medicine, " other"or "I don't know." Finally, they valued ten motivational factors. Results: Forty percent of the medical students reported no specialty preference yet. Taken together, female medical students preferred pediatrics and wished to combine work and care, whereas male students opted for surgery and valued career opportunities. Conclusions: Gender-driven professional preferences in new medical students should be noticed in order to use competencies. Changes in specialty preferences and motivational factors in pre- and post graduates should further assess the role of medical education.