The universally controversial issue of deaths in custody is especially pertinent to South Africa. This study was prompted due to the increasingly diminishing ability for a concerted effort at tackling this issue by all parties involved. The 5 year retrospective, descriptive case audit performed at the Pretoria Medico-Legal Laboratory aimed to evaluate the current medico-legal investigation of deaths in custody in Pretoria, South Africa. Over half of the deaths (52%) occurred as a result of police action, 30% in police custody and 18% in correctional services custody. Gunshot wounds and hangings were the number 1 and 2 most common causes of death, respectively, with homicide and suicide being the 2 most common manners of death, respectively. The principal conclusion from the results is the presence of a flawed and malfunctioning medico-legal investigation system. The introduction of a formal protocol is urgently required to provide a framework for these investigations.