This study evaluates the degree of empathy among medical students and its influencing factors at three critical moments of their degree studies (beginning of first year and end of third and sixth years) as well as establishes low-, medium-, and high-empathy cut-off points to obtain valid and reliable results that can be extrapolated to the general population. This cross-sectional study of the eight (public and private) medical schools in the province of Madrid, used an electronic questionnaire with the Jefferson Scale of Empathy (JSE), Medical Student Well-Being Index, and other independent characteristics as measuring instruments. Of the 2,264 student participants, 1,679 (74.0%) were women, with a 50.7% participation rate. No significant differences were found in empathy levels by academic year. Regarding range, percentile and cut-off point tables were established to identify students with high, medium, and low empathy levels. Women (p<0.001), volunteer workers (p<0.001), and those preferring general specialties (internal medicine, psychiatry, pediatrics, or family medicine) scored higher on the JSE (p<0.02). Moreover, 41.6% presented high level of psychological distress. Women reported a lower well-being level and a higher risk of psychological distress (p = 0.004). In sum, the empathy of medical students in Madrid did not differ among the three critical moments of their university studies. The established cut-off points could be taken into account when accessing the medical degree and identifying students with low levels of empathy to implement curricular interventions to rectify this perceived deficiency. There was a high percentage of medical students with high levels of psychological distress.