Empathy in medical students is receiving increasing attention as it is fundamental to build and develop a functional patient-physician relationship. When looking at its determinants, demographic and academic factors seem to concur in shaping empathy in this population. Although data show strong gender differences and changes in empathy throughout medical school, it is not clear the direction of these changes and whether gender and curriculum features modulate them. This longitudinal study examined changes in empathy and explored gender differences throughout the medical school. Four consecutive cohorts of Italian medical students ( = 336) completed the Jefferson Scale of Empathy - Student (JSE-S) and the Interpersonal Reactivity Index (IRI) in their second year of study (before any clinical clerkship and communication skills courses) and fifth year of study (after a 2-year clinical clerkship and communication skills courses). Analysis of variance for repeated-measures revealed that, beyond the effect of gender, JSE-S total score and IRI Perspective Taking increased, whereas IRI Personal Distress and IRI Fantasy significantly decreased throughout medical school. No significant change in IRI Empathic Concern emerged over time. Student's -tests showed that female students displayed significantly higher mean scores than their male counterparts for all empathy measures in both their second and fifth years of medical training. The findings suggest that the medical curriculum affects self-reported empathy dimensions among undergraduate medical students. Further research is needed to deepen the understanding of the educational factors that promote the changes in empathy levels during medical training.