Sorghum plays an important role in food security in Africa where it serves as the staple food for millions of people. The crop, however, is susceptible to infection by mycotoxigenic fungi such as Aspergillus flavus, A. parasiticus, Fusarium andiyazi, F. thapsinum, F. verticillioides and F. proliferatum. This can lead to a reduction in yield and the production of aflatoxin and fumonisin that are harmful to humans and animals. Sorghum grain samples were collected from five cultivars planted at 21 localities in South Africa from 2007-2009. Each sample was subjected to quantitative (q) real-time-PCR to determine the presence and biomass of aflatoxin-producing Aspergillus spp. and fumonisin-producing Fusarium spp. Aflatoxin and fumonisin amounts were also quantified by means of High Performance Liquid Chromatography (HPLC). HPLC results yielded minute amounts of aflatoxin with little or no fungal contamination determined with qPCR. The soft grain genotype NS5511 was more prone to aflatoxin contamination than the other cultivars. Fumonisin-producing Fusarium spp. were absent from sorghum samples collected in 2007. In 2008, sorghum samples from the Northwest and Kwa-Zulu Natal Provinces had small amounts of fungal contamination. In 2009, a low amount of fungi from samples from Northwest, Kwa-Zulu Natal and the Free State Provinces were recorded. Although small amounts of fungi were present, fumonisin were not produced. HPLC and qPCR results indicate that Aspergillus and Fusarium spp. and their mycotoxins do not pose a threat to sorghum production in South Africa