This article reports the results of an investigation to identify the disciplinary strengths and the international standing of the higher education institutions in South Africa. Even though comparative assessments provide valuable information for research administrations, researchers and students such information is not available in South Africa currently. The Essential Science Indicators database of the Institute for Scientific Information is utilized for the investigation and six South African universities are identified to be included in the top 1% of the world's institutions cited in the international scientific literature. The identified institutions are University of Cape Town, University of Pretoria, Orange Free State University, University of Witwatersrand, University of Natal and University of Stellenbosch. Analysis of the scientific disciplines in which the South African institutions meet the threshold requirements for inclusion in the database shows that the country has citation footprints in only nine of the 22 broad scientific disciplines. The article identifies the international standing of the South African universities in the various scientific disciplines, and elaborates on the consequences relevant to higher education and science and technology policy.