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Introduction Traumatic injuries to the lower gastrointestinal tract (rectum and anus) have been largely reported in the military setting with sparse publications from the civilian setting. Additionally, there remains a lack of international consensus regarding definitive treatment pathways. This systematic review aimed to assess the current literature and propose a standardised treatment algorithm to aid management in the civilian setting. Methods A systematic review of available literature from 1999 to 2016 that was performed. Primary endpoints were the assessment and surgical management of reported rectal and anal trauma. Results Seven studies were included in this review, reporting on 1255 patients. 96.3% had rectal trauma and 3.7% had anal trauma. Gunshot wounds are the most common mechanism of injury (46.9%). The overwhelming majority of injuries occurred in males (>85%) and were associated with other pelvic injuries. Surgical management has substantially evolved over the last five decades, with no clear consensus on best management strategies. Conclusion There remains significant international discrepancy regarding the management of penetrating trauma to the rectum. Key management principals include the varying use of the direct primary closure, faecal diversion, pre-sacral drainage and/or distal rectal washout (rarely used). To date, there is sparse evidence regarding the management of penetrating anal trauma.