Fumonisins are secondary, carcinogenic metabolites produced primarily by Fusarium verticillioides and Fusarium proliferatum on maize worldwide. The natural occurrence of fumonisin-producing Fusarium spp. and fumonisin contamination of maize grain were quantified in selected maize cultivars from principal production areas of South Africa. Grain colonization by Fusarium spp. was determined using quantitative real-time PCR (qPCR) and contamination with fumonisins using HPLC analysis. Kernels from the 2007 samples were also plated onto Fusarium selective medium and subsequently, split plates containing PDA & CLA. The number of fumonisin producing Fusarium spp. were quantified and microscopically identified after 14 days. Simple linear regression analysis was used to determine the relationship between target DNA, fumonisins and the number of fumonisin producing Fusarium spp. using the plating out method. Results indicated high natural infection by fumonisinproducing Fusarium spp. and fumonisin concentrations in warmer production areas such as Northern Cape, North West and Free State Provinces. Spearman Ranking Correlations indicated that the responses of cultivars to colonization of grain by fumonisin producing Fusarium spp. varied over localities/seasons (r s =0.42 to 0.64) suggesting that cultivars reacted differently to different environmental/inoculum conditions (disease potentials). Cultivars CRN3505 and DKC80-12B showed a degree of resistance to fungal infection. As with fungal colonization, Spearman Rank Correlations indicated the response of cultivars to fumonisin contamination to vary over localities/ seasons (r s =0.29 to 0.70). Cultivars DKC80-12B and LS8521B showed a degree of resistance to fumonisin contamination. Regression analysis yielded a significant relationship between HPLC data and qPCR, but not with the plating out of grain data suggesting the former to be a better indicator of potential fumonisin contamination. Site-specific, daily maximum temperature and rainfall data were provided by the ARC-Institute for Soil Water and Climate's meteorology office. No significant relationship between these weather parameters and colonization of grain by fumonisin producing Fusarium spp. was recorded, although a tendency was observed between fumonisin contamination and mean maximum temperature.