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This longitudinal study was designed to examine changes in medical students’ empathy during medical school and to determine when the most significant changes occur.Four hundred fifty-six students who entered Jefferson Medical College in 2002 (n = 227) and 2004 (n = 229) completed the Jefferson Scale of Physician Empathy at five different times: at entry into medical school on orientation day and subsequently at the end of each academic year. Statistical analyses were performed for the entire cohort, as well as for the “matched” cohort (participants who identified themselves at all five test administrations) and the “unmatched” cohort (participants who did not identify themselves in all five test administrations).Statistical analyses showed that empathy scores did not change significantly during the first two years of medical school. However, a significant decline in empathy scores was observed at the end of the third year which persisted until graduation. Findings were similar for the matched cohort (n = 121) and for the rest of the sample (unmatched cohort, n = 335). Patterns of decline in empathy scores were similar for men and women and across specialties.It is concluded that a significant decline in empathy occurs during the third year of medical school. It is ironic that the erosion of empathy occurs during a time when the curriculum is shifting toward patient-care activities; this is when empathy is most essential. Implications for retaining and enhancing empathy are discussed.