Introduction: the mental health of medical students has been extensively researched, showing that they are part of a group vulnerable to the development of mental disorders. Aim: the aim of this research was to determine the frequency of NSSI and its associated factors in medical students in Paraguay. Methodology: this was a descriptive and cross-sectional study. An online survey was launched to assess depression, anxiety, and self-harm, the PHQ-2, the GAD-7 and SHQ scales were used, respectively. Results: we received responses from 330 medical students. Of the participants, 71.2 % were female. 46.4% of the participants were identified as having depression (PHQ-2 ≥ 3) and 37.3 % as having anxiety (GAD-7 ≥10). The frequency of NSSI was 27 % (n = 89). The main factors associated with NSSI were a previous diagnosis of a mental disorder (which increased the likelihood of NSSI by 3.76 times) and/ or a history of physical or sexual abuse (with a 3.75-fold increase). Conclusion: this research found the presence of NSSI in almost 3 out of 10 of the medical students surveyed. The main factors associated with self-injurious behavior were a previous diagnosis of a mental disorder and/or a history of physical or sexual abuse.