Objectives Little is known about the relationship between the career preferences of medical students and the medical schools at which they are enrolled. Our aim was to explore this relationship early in students' medical training. Methods Year1 (2009-2010) medical students at the five Scottish medical schools were invited to take part in a career preference questionnaire survey. Questions were asked about demographic factors, career preferences and influencing factors. Results The response rate was 87.9% (883/1005). No significant differences were found among medical schools with regard to first-choice specialty. Surgery (22.5%), medicine (19.0%), general practice (17.6%) and paediatrics (16.1%) were the top career choices. Work-life balance, perceived aptitude and skills, intellectual satisfaction, and amount of patient contact were rated as the most important job-related factors by most respondents. Few differences were found among schools in terms of the impact of job-related factors on future career preferences. Students for whom the work-life balance was extremely important (odds ratio [OR]=0.6) were less likely to prefer surgery. Students for whom the work-life balance (OR=2.2) and continuity of care (OR=2.1) were extremely important were more likely to prefer general practice. Conclusions Students' early career preferences were similar across the five medical schools. These preferences result from the interplay among demographic factors and the perceived characteristics of the various specialties. Maintaining a satisfactory work-life balance is very important to tomorrow's doctors, and the data hint that this may be breaking down some of the traditional gender differences in specialty choice. Longitudinal work is required to explore whether students' career preferences change as they progress through medical school and training.