This is one of the first studies to explore the experiences and expressions of discrimination, violence and exclusion based on genders, sexualities and the bodies in Physical education (PE) in Japan. Through this research, we hope to gain insight into the gender and sexual politics of Japanese PE. The study was administered in three Japanese universities in 2017. Based on 979 survey responses, we present a preliminary analysis of students reported the experiences of discrimination and exclusion. We conducted the quantitative and qualitative content analysis of 410 (41.9%) survey responses, which answered the open-ended question about negative experience in PE. By using quantitative content analysis software (KH coder), we extracted seven clusters: 1) being scolded for a mistake, 2) being a nuisance to a partner or a team, 3) forced to perform (play) sport or do exercise, 4) swimming, 5) running, 6) class (teaching) methods, and 7) methods of evaluation. The main factors that caused the negative experience are codified to: classmates (category 1), oneself (category 2), teachers (category 3, 6, 7) and exercise characteristics (category 4, 5). When analyzed the result by gender, “normative woman” (cis-gendered, heterosexual) tends to be ashamed that they are not good at sports and their self-respect becomes wounded. On the other hand, “normative man” (cis-gendered, heterosexual) tends to remember the negative experience as those moments when they were blamed by their classmates. The persons of “non-normative” gender/sexuality (transgender and/or non-heterosexual) tend to have more negative experiences based on heterosexism and binary gender system. Our findings suggest that the evaluation criteria set by the curriculum and/or teacher need to be changed. Because the criteria made students’ achievement (or the lack thereof) visible, it leads to the bodily hierarchy. This hierarchy push students who are not athletic into a lower position and marginalize them in the classroom.