Mycotoxins are toxic fungal secondary metabolites that contaminate an estimated 25% of foods globally. Aflatoxin and fumonisin are major mycotoxins that contaminate maize in tropical countries. Kenya's frequent aflatoxicosis outbreaks and the associated human fatality rates have received global attention. The objective of this dissertation was to investigate the extent and the drivers for mycotoxin contamination in Kenyan maize. Between May 2009 and March 2010, surveys were conducted in three provinces (Rift Valley, Western and Nyanza) of western Kenya, the country's grain basket and a region where mycotoxin outbreak had not been recognized. Aflatoxin contamination above the regulatory limit of 10 ppb was observed in 15% of the flour samples that had been collected from the patrons of local mills. Drought and monocropping were identified as drivers for increased aflatoxin contamination. A longitudinal survey in farmers' storage sheds and at local mills in Western Province revealed vulnerability of the most popular varieties to mycotoxins. Surveys were conducted in 10 districts of Eastern Province during an aflatoxin outbreak in 2010. Aflatoxin contamination above 10 ppb was observed in 39% of the flour samples from patrons (n=1500) of local mills, while 37% were above the 1 ppm regulatory limit for fumonisin. Reduced aflatoxin accumulation was associated with intercropping, larger farms and high grain yield. Visual grain sorting reduced fumonisin but not aflatoxin levels. Analysis of aflatoxin in naturally-infected diverse maize germplasm grown in eastern Kenya showed higher contamination under low nitrogen (N) than under optimal N. Early-maturing maize had reduced aflatoxin accumulation under low N, possibly because of faster utilization of the limiting and diminishing soil N. A mature kernel screening assay of diverse maize inbred lines showed that colonization and aflatoxin accumulation were influenced by the ear environment (where maize were grown). High sulfur content in grain was associated with reduced kernel colonization and aflatoxin accumulation. Management strategies should include: 1. surveillance across all maize-producing regions, 2. breeding for early maturing maize, and 3. spectral grain sorting. Experiments should be conducted to identify the intercrop species and the mechanism for aflatoxin control, and to elucidate the maize ionome - mycotoxin relationship. iii