The aim was to study discrimination, with a focus on gender and sexual harassment among medical students at Uppsala University in Sweden. A survey was sent via email to all registered medical students in the spring semester of 2020. Data were compared with two previous studies. Questions about gender and sexual harassment were the same as in the study conducted in 2002 and 2013. In addition, the 2020 survey included a question about other grounds of discrimination. Forty percent, that is, 453 out of 1,130 medical students, participated. The proportion of students reporting gender-based discrimination during the preclinical semesters was similar for females and males. During the clinical semesters, significantly more females than males reported gender discrimination (41% vs. 21.5%, p = 0.005) and sexual harassment (22% vs. 5%, p = 0.001). Physicians were the most commonly reported perpetrator. Reports about not being respected had increased from 2% to 20% between 2013 and 2020 among female clinical students. The prevalence of those who experienced several sexually harassing behaviors increased for the female and male clinical students and the female preclinical students. Receiving an unwelcome touch increased from 1% to 7% for the female clinical students. Discrimination due to ethnicity was reported by 36% of the students born in a country other than Sweden compared to 3% of those born in Sweden. Our findings confirm that experiences of different forms of discrimination exist in this medical school, and females and minorities are particularly affected.