BACKGROUND: It is known that male and female medical students have different experiences in their clinical training. Aims: To assess whether male and female medical students change in their self-rated work habits and interpersonal habits during the first year of clinical training. METHOD: Longitudinal study of self- and peer-assessment among 224 medical students in 3 consecutive classes at a private US medical school. Students rated themselves on global work habits (WH) and interpersonal attributes (IA). Students also rated and were rated by 6-12 peers on the same scale. RESULTS: In the second year of medical school, there were no differences between men and women in quartiles of self-assessed WH or IA. At the end of the third year, however, women were more likely to be in the lower quartiles of self-assessed WH (X(2) = 6.77; p = 0.03), as well as the highest quartiles of self-assessed IA (X(2) = 11.36; p = 0.003). In both years, women rated their own WH skills significantly lower than they rated their peers, while men rated themselves similarly to peers. There were no sex differences in self-assessed IA. CONCLUSIONS: Although second-year male and female medical students appear similar to one another in terms of self-assessed WH and IA, by the end of the third year women rate themselves relatively lower in WH, while men rate themselves relatively lower in IA.