Physician gender is associated with differences in the male-to-female ratio between specialities and with preferred working hours. We explored how graduating students’ sex or full-time or part-time preference influences their speciality choice, taking work-life issues into account. Graduating medical students at Radboud University Medical Centre, the Netherlands participated in a survey (2008–2012) on career considerations. Logistic regression tested the influence of sex or working hour preference on speciality choice and whether work-life issues mediate. Of the responding students (N = 1,050, response rate 83, 73.3 % women), men preferred full-time work, whereas women equally opted for part time. More men chose surgery, more women family medicine. A full-time preference was associated with a preference for surgery, internal medicine and neurology, a part-time preference with psychiatry and family medicine. Both male and female students anticipated that foremost the career of women will be negatively influenced by family life. A full-time preference was associated with an expectation of equality in career opportunities or with a less ambitious partner whose career would affect family life. This increased the likelihood of a choice for surgery and reduced the preference for family medicine among female students. Gender specifically plays an important role in female graduates’ speciality choice making, through considerations on career prospects and family responsibilities.