Although empathy is considered one of the essential attributes of professionalism for medical students, the empathy level of the Saudi medical students was not assessed till now while it was assessed worldwide. This study aimed to determine the level of empathy among medical students in different study years at Faculty of Medicine (FOM), King Abdulaziz University (KAU), Jeddah, and to explore in depth the factors that affect it. This comparative cross sectional study used a translated Arabic version of the Jefferson Scale of Physician Empathy-student version (JSPE-SV). It was distributed to all medical students in different study years at KAU during the academic year 2014-2015 and the response rate was 58.3 %. Data were collected and analyzed using the statistical package of Social sciences (SPSS) version 22. The mean empathy score was 106.55±19.16 and it was higher, but nonsignificant, in females than males. It increases along with the study year and its level among the 6th year students was significantly higher (p=0.004) than that of the 2nd year. Intact marital status of parents (p=0.012), satisfactory relationship with mother and father (p=0.009, p=0.012), having a patient in the family (p=0.002) were significantly associated with higher empathy level. Students empathy level was relatively low but it was increasing throughout the study years denoting the positive impact of the medical curriculum. More highlights on the patients physician relationship all through the medical curriculum is needed to emphasize and promote empathy of the student.