Mycological (mycotoxigenic Fusarium and aflatoxigenic Aspergillus spp.) and multiple mycotoxins [aflatoxin B1 (AFB1), fumonisin B (FB), deoxynivalenol and zearalenone] surveillance was conducted on raw whole grain sorghum (Sorghum bicolor) and pearl millet (Pennisetum glaucum) produced on smallholder farms, and processed products sold at open markets in northern Namibia. Fungal contamination was determined with morphological methods as well as with quantitative Real-Time PCR (qPCR). The concentrations of multiple mycotoxins in samples were determined with liquid chromatography tandem mass spectrometry. The incidence of mycotoxigenic Fusarium spp., Aspergillus flavus and A. parasiticus, as well as the concentrations of AFB1 and FB were significantly (P