Maize is the staple food of South Africa and its cultivation covers the largest area of farmland in the country. It plays an important role in the economy as South Africa is consuming 10 million tons of maize per annum. Most South Africans consume maize in some form or another. This commodity has regularly been associated with mycotoxigenic fungi and in some cases their respective mycotoxins. The problem is not only confined to the borders of South Africa but is a concern worldwide. Mycotoxins are known to affect both human and animal health. Some of the most well known mycotoxins are the fumonisins, deoxynivalenol and trichothecenes produced by Fusarium spp., aflatoxins and ochratoxin A produced by mostly Aspergillus spp., as well as patulin and citrinin that are produced by mainly Penicillium spp. Mycotoxins acting together and individually can be hepatotoxic, carcinogenic and teratogenic to humans and animals. The main objective of this study was to screen commercially produced maize cultivars in South Africa that would be either resistant to, or have a slower infection rate when inoculated with the ten selected mycotoxigenic fungi from South African maize. The objective was also to develop a method to detect and identify these mycotoxigenic fungi in the infected maize cultivars, using both basic microbiological and molecular means. These objectives were achieved by a series of experiments that are outlined in the individual chapters. The first part of this study evaluated the level of infestation of fungi in all the commercially produced maize cultivars in South Africa. A basic fungal enumeration and identification was carried out. This allowed the comparison of the in vivo ability of the selected cultivars to endure the natural invasion of mycotoxigenic fungi during cultivation in the same area namely Potchefstroom. As part of the maize evaluation, the cultivars were artificially inoculated with ten selected mycotoxigenic fungi, which consisted of five field fungi nl. Alternaria alternata, Fusarium graminearum, Fusarium verticillioides, Phoma sorghina and Stenocarpella maydis, and five storage fungi nl. Aspergillus flavus, Aspergillus ochraceus, Eurotium repens, Penicillium islandicum and Rhizopus oryzae under storage conditions. The ability of certain maize cultivars to resist the infestation by mycotoxigenic fungi under storage conditions was demonstrated. The second part of this study was to use basic molecular methods to detect and identify the ten mycotoxigenic fungi in the infected maize. This was done by making use of the sequence variations of the internal transcribed spacer (ITS) and D1/D2 regions of the fungal rRNA gene. Results showed that the ITS region gave better differentiation and in most cases allowed identification of the mycotoxigenic fungi. The application of the combined use of microbiological and molecular methodology for the detection and identification of mycotoxigenic fungi in maize by testing laboratories in South Africa were outlined in the final chapter. Implementation of a plan to evaluate maize cultivars in the pre-planting, harvesting and storage phases, can provide a holistic overview of the commodity and can be further implemented in the rural areas.