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Maize is a staple crop in rural subsistence regions of southern Africa, is mainly produced for direct household consumption and is often contaminated with high levels of mycotoxins. Chronic exposure to mycotoxins is a risk factor for human diseases as it is implicated in the development of cancer, neural tube defects as well as stunting in children. Although authorities may set maximum levels, these regulations are not effective in subsistence farming communities. As maize is consumed in large quantities, exposure to mycotoxins will surpass safe levels even where the contamination levels are below the regulated maximum levels. It is clear that the lowering of exposure in these communities requires an integrated approach. Detailed understanding of agricultural practices, mycotoxin occurrence, climate change/weather patterns, human exposure and risk are warranted to guide adequate intervention programmes. Risk communication and creating awareness in affected communities are also critical. A range of biologically based products for control of mycotoxigenic fungi and mycotoxins in maize have been developed and commercialised. Application of these methods is limited due to a lack of infrastructure and resources. Other challenges regarding integration and sustainability of technological and community-based mycotoxin reduction strategies include (i) food security, and (ii) the traditional use of mouldy maize.