M.Tech. (Biomedical Technology) / A study was conducted to determine the extent of fungi and mycotoxins contamination of Rwandan selected food commodities. A total of one-hundred food samples including maize, rice, cassava, beans and peanuts were collected from all five provinces of Rwanda and analysed. Mycological data obtained revealed a high level of contamination of common toxigenic fungi belonging mainly to the Aspergillus, Penicillium and Fusarium genera. Accordingly, Aspergillus flavus was the most prevalent fungal contaminant in maize (90%), while A. carbonarius was mainly concentrated in peanuts at an incidence rate of 70%. Aspergillus fumigatus was mostly found in cassava (85%) in combination with Penicillium decumbens at the rate of 70%, meanwhile P. citrinum was found at an incidence rate of 80% in rice. The genus Fusarium was dominantly present with F. verticillioides and F. graminearum found in all analysed commodities. A toxigenicity study was also conducted to evaluate the capacity of these fungi recovered to produce their respective mycotoxins. Certain species such as A. flavus and A. parasiticus isolated from these commodities produced the aflatoxins (AFs). Other Aspergillus spp. such as A. carbonarius produced ochratoxin A (OTA) and F. verticillioides and F. graminearum also showed their capacity in producing different mycotoxins viz: zearalenone (ZEA), fumonisins (FBs) and deoxynivalenol (DON). The analysis of mycotoxins in these commodities was performed following thin layer chromatography (TLC) and high performance liquid chromatography (HPLC). Data obtained revealed that peanuts and maize were the most contaminated with mycotoxins at incidence rates of 85 and 80%, respectively, and at the highest contamination levels. The highest AF-contaminated commodity was maize from Western province (range: 1.3-3219.6 μg/kg; mean: 829.3 μg/kg) followed by peanut from the same region whose mean level found was 401.5 μg/kg (range: 3.2–1755.8 μg/kg). Ochratoxin A was also found in peanuts with a mean concentration of 302.6 μg/kg, while DON was found at the highest level of 419.6 μg/kg in a rice from Kigali-city. Maize was the main substrate for FBs (mean: 134 μg/kg; max: 4591 μg/kg). Zearalenone was also recovered from samples but at a low incidence rate of 40% with the highest level of 5.2 μg/kg recorded. It was also observed that 65% of samples analysed were contaminated with more than one mycotoxin.