Objective: To estimate the prevalence of depression and abuse and identify the associated factors in medical interns in Peruvian hospitals. Methods: We conducted a multicentre, cross-sectional and analytical study during the months of March to May 2016. We included medical interns from 18 Peruvian hospitals, in Lima and provinces. We used a survey that included sociodemographic data and a scale to measure the perception of abuse (psychological, physical and sexual). In addition, we used the Spanish version of the PHQ-9 to evaluate depression. We used Poisson regression with robust variances to calculate prevalence ratios (PRs). Results: A total of 402 medical interns participated in the study, the median age was 25 [IQR: 21–33], and 52.7% were male. Moreover, 25.4% of them suffered from depression. In the adjusted model, the variables associated with depression were age (PRa = 1.15), the number of hours they sleep per day (PRa = 1.23), being a woman (PRa = 3.33), performing the internship in a province (PRa = 0.25), studying at a public university (PRa = 0.64), living with parents (PRa = 0.65) or alone (PRa = 0.33), and having perceived some type of abuse (PRa = 1.07). Conclusions: A quarter of surveyed medical interns had depression. Early screening is necessary to identify perceived abuse and other triggering depression factors that may adversely affect work performance and overall mental health during medical internships.