The maltreatment and torture of prisoners constitute a global problem. Methods of maltreatment are classified as the psychological and the physical, and physical methods inevitably lead to psychological sequelae. Our review offers an analysis from the medico-legal perspective of the literature on the torture and physical and sexual abuse experienced by prisoners and their psychological sequelae and aims to investigate the medico-legal issues of investigating maltreatment in prison so as to suggest methodologies and updated approaches for dealing with such cases in a forensic context. We performed a comprehensive literature search of peer-reviewed publications (articles and reviews), research reports, case studies, books, service models, protocols, and institutional documents available online using key electronic databases (Scopus, PubMed) and search engines (Google Scholar) with the following keywords: physical violence, psychological violence, torture, maltreatment, physical abuse, psychological abuse AND prison OR prisoner OR jail OR custody. In the medical literature, most of the publications on torture are based on retrospective studies of torture among survivors and often refer to asylum seekers. Forensic evaluation is crucial for assessing the determinant elements of torture and maltreatment. A multidisciplinary approach and standardized and updated methodologies are needed to support policymakers, national institutions, and public health system initiatives in this field.