Background: Clinical experience is considered to affect medical students' career preferences. It is not known whether the sequence of the clinical rotations influences these preferences. Aim: To explore whether the first clinical clerkship has more impact on career preference than the second by examining the association between the first clinical clerkship and the choice of an elective sixth-year internship. Method: University Medical Center Utrecht students are assigned to either a surgical or a medical ward for the first third-year clerkship and to the other ward for the second clerkship. In a retrospective cohort study, internship data of 488 sixth-year students were related to their first clerkship 3 years earlier. Results: For the group as a whole, no association was found between third-year clerkship and sixth-year internship. However, male students who had been assigned to surgery first more often chose a surgical internship than those who had been assigned to medical clerkship first and vice versa (p < 0.02). Within the female subgroup, no association was found. Conclusion: A positive association between the nature of the clerkship and the sixth-year internship preference among male students suggest that the first clinical experience can affect later specialty preference.