Background: Health services for victims of rape are recognised as a particularly neglected area of the health sector internationally. Efforts to strengthen these services need to be guided by clinical research. Expert medical evidence is widely used in rape cases, but its contribution to the progress of legal cases is unclear. Only three studies have found an association between documented bodily injuries and convictions in rape cases. This article aims to describe the processing of rape cases by South African police and courts, and the association between documented injuries and DNA and case progression through the criminal justice system., Methods and Findings: We analysed a provincially representative sample of 2,068 attempted and completed rape cases reported to 70 randomly selected Gauteng province police stations in 2003. Data sheets were completed from the police dockets and available medical examination forms were copied. 1,547 cases of rape had medical examinations and available forms and were analysed, which was at least 85% of the proportion of the sample having a medical examination. We present logistic regression models of the association between whether a trial started and whether the accused was found guilty and the medico-legal findings for adult and child rapes. Half the suspects were arrested (n = 771), 14% (209) of cases went to trial, and in 3% (31) of adults and 7% (44) of children there was a conviction. A report on DNA was available in 1.4% (22) of cases, but the presence or absence of injuries were documented in all cases. Documented injuries were not associated with arrest, but they were associated with children's cases (but not adult's) going to trial (adjusted odds ratio [AOR] for having genital and nongenital injuries 5.83, 95% confidence interval [CI] 1.87-18.13, p = 0.003). In adult cases a conviction was more likely if there were documented injuries, whether nongenital injuries alone AOR 6.25 (95% CI 1.14-34.3, p = 0.036), ano-genital injuries alone (AOR 7.00, 95% CI 1.44-33.9, p = 0.017), or both nongenital and ano-genital injuries (AOR 12.34, 95% CI 2.87-53.0, p = 0.001). DNA was not associated with case outcome., Conclusions: This is the first study, to our knowledge, to show an association between documentation of ano-genital injuries, trials commencing, and convictions in rape cases in a developing country. Its findings are of particular importance because they show the value of good basic medical practices in documentation of injuries, rather than more expensive DNA evidence, in assisting courts in rape cases. Health care providers need training to provide high quality health care responses after rape, but we have shown that the core elements of the medico-legal response require very little technology. As such they should be replicable in low- and middle-income country settings. Our findings raise important questions about the value of evidence that requires the use of forensic laboratories at a population level in countries like South Africa that have substantial inefficiencies in their police services. Please see later in the article for the Editors' Summary.