Fumonisin occurrence was investigated in subsistence maize in four rural villages in each of Mbizana and Centane areas, South Africa. Samples (total 211) were analysed morphologically for Fusarium species and by high performance liquid chromatography for fumonisins. The mean incidence levels of Fusarium verticillioides in Centane good maize were 16% for both 1997 and 2000, but increased to 32% in 2003, whereas Mbizana good maize contained levels of 17% and 11% (2000 and 2003 seasons, respectively). The mean total fumonisin level in good maize in Centane for 1997 and 2000 was 575 and 975 µg/kg and 2150 µg/kg in 2003. In Mbizana, the mean total fumonisin level in good maize for 2000 was 950 µg/kg, but decreased to 610 µg/kg in 2003. The 2003 drought conditions led to a substantial increase in fumonisin levels in dry subhumid Centane, compared to humid subtropical Mbizana. This study emphasises the seasonal fluctuation in fumonisin levels.