Medical and health sciences institutions and organisations are faced with challenges in resource allocation for research and publishing. The aim of this study was to retrospectively analyse South African publication trends in medicine to provide guidance for future strategic planning in academic medicine. We used the Scimago database spanning the years 1996-2011 to analyse South African publication outputs in a number of categories in medicine, as defined in the Scopus database. The data reveal a number of significant growth areas but also reveal areas that should potentially be growing but remain static. In some areas, growth has aligned with the expectations of health and disease trends, but other areas, in which growth would have been expected, have remained static. Interesting features are also revealed when the data are compared with those of other developed and developing countries. For 1996-2011, South African medical publication output ranked 33 in the world based on the number of publications, but 28 based on the h-index. Interestingly, whilst South Africa produced less than 25% of the output of India, the h-index for South Africa is 153 compared with 145 for India. South Africa's medical publication output has steadily increased over the 14-year period but the number of citations per document has declined. This analysis provides a useful strategic overview for medical institutions and government funding organisations to guide the allocation of research budgets and resources in a discipline- or category-specific manner to influence research outputs.