Mistreatment of medical students has long been a challenge in medical schools of various countries. However, studies assessing the prevalence and its effects on students' perceptions of their professional development are scant in Ethiopia. Thus, this study is an attempt to contribute empirical evidence to fill this gap. Specifically, the paper probes the prevalence of exposure to mistreatment among intern medical students at St. Paul Hospital Millennium Medical College, Addis Ababa, Ethiopia. Both quantitative and qualitative data were collected from primary and secondary source. The data collected were analyzed and discussed using several descriptive statistics. The survey result revealed the presence of different types of mistreatment, which fairly varies between male and female students. The most important ones were yelling or shouting that is offensive, harsh, or insulting speech on both male and female students and some sort of sexual harassment in only female students. Threat to unfair grade and giving some kind of negative or disparaging remarks are also types of mistreatments (closer to often) perceived and reported by students. The paper also find evidence that nurses and residents were most important source of mistreatment in the learning environment. However, the reasons for such unprofessional conducts were not very clear to most of them. The perceived effect of one or more types of mistreatments were also analyzed and the result shows that medical students who experience mistreatment are found to have hurtful outcomes on their emotional security and professional attitudes. Specifically, many students indicated to sometimes feel a sense of regret in choice of career or lack of satisfaction their educational experience, hating the health environment and depression and low self-confidence. Such feelings of distress during intern status of studies could exacerbate the compromising quality of potential physicians and health care system. Qualitative analysis of data was also highly consistent with the above findings and used for triangulation purpose. The study concludes by highlighting some short- and long-term recommendations that can help the school develop policies and eradicate the widespread and complex mistreatment phenomenon.