Traditional medicine is an important aspect of healthcare delivery in South Africa and is used by at least 70% of the country's population. The trade in medicinal plants is a multi-million rand business which is a major driver for rural economies. However, the conditions in which these plant products are transported and stored make them prone to fungal contamination which results in economic losses to the traders and pose potential health hazards to consumers. Of major concern is the possible presence of toxigenic fungi and mycotoxins. This study assessed fungal and mycotoxin contamination of African herbal products sold in Cape Town and Tshwane (formerly Pretoria) in South Africa. Of the 16 samples analyzed, 15 were contaminated with at least one of these three fungal genera: Aspergillus, Fusarium, and Penicillium. Fumonisin B(1) was present in 13 of the samples in quantities ranging from 14 to 139 microg/kg (detection limit 5 microg/kg). None of the samples was contaminated with aflatoxigenic fungi or aflatoxin (detection limit 0.5 microg/kg). This is the first study to report on mycological and mycotoxin contamination of commercial traditional African medicines in South Africa. There is a need to expand the study to other urban centers to gain enough insight into this problem and then to intervene with measures that can protect the public from potential harm.