Background: The Mediterranean Diet (MeDi) is associated with a reduced risk of several non-communicable chronic diseases. High levels of nutrition knowledge are associated with greater MeDi adherence irrespective of education and other socio-economic factors. The present study investigates whether attending medical school changes students’ adherence to the MeDi. Methods: A cross-sectional study was conducted in November–December 2014 using the 16-item KIDMED questionnaire, which inquiries into eating habits. Each respondent’s KIDMED index (range 0–12), whose scores reflect ‘poor’, ‘average’ or ‘good’ MeDi adherence, was calculated. Scores were analyzed for gender, age and early/late medical school year. The Mann–Whitney U-test and the chi-square test were used for group comparisons. Ordinal logistic regression was applied to estimate the odds ratio (OR) and 95% confidence interval (CI) for changes in MeDi adherence from early to late medical school after adjustment for potential confounders. Results: Participants were 1038 medical students (573 females) aged 18–34 years (mean 21.9 ± 2.4). There were 20.8% ‘poor’, 56.5% ‘average’ and 22.7% ‘good’ scores. Gender significantly affected scores (P < 0.01). In the ordinal logistic regression model the odds for greater MeDi adherence increased for the female gender (P < 0.05); females were 48% more likely to have a ‘good’ KIDMED score than their male peers, whereas early/late medical school year did not affect results [adjusted odds ratio (OR) = 0.95; P = 0.15]. Conclusions: More than 70% of our medical students know very little about healthy eating and the MeDi. However, this knowledge is essential in their future profession both to support therapeutic decision-making and effective preventive actions.