Maize and groundnuts are traditional nutrient-rich and high economic value foods grown in Uganda. However, these crops are susceptible to aflatoxin contamination which may result into aflatoxicosis related illnesses. Occurrence of flatoxins in the foods varies across food value chains, gender and agro-ecological zones of Uganda. Therefore, we conducted a cross-sectional study in 80 maize and groundnut foodstuff from Masindi and Soroti agro-ecological districts respectively. We determined levels of total aflatoxins in maize and groundnut samples across food value chains, gender and agro-ecological zones. This was aimed at assessing safety and quality status of the foods in Uganda. Questionnaires were administered to obtain information on food handling practices. 500g of each food sample were obtained and analyzed for total aflatoxin levels using ELISA assay. Data was analyzed using descriptive and analytical statistics. In overall, 45% of maize and 30% of groundnut foods were contaminated with aflatoxins. Mean aflatoxin levels in foods from Eastern and Western agro-ecological zones were 0.052±0.036ppb and 0.045±0.033ppb respectively (p=0.124). Mean aflatoxin levels in groundnuts from both male and female respondents were coincidentally 0.052ppb. Whereas, the mean aflatoxin levels in maize from male and female respondents were 0.056±0.037ppb and 0.039±0.029ppb respectively. Across the food value chain, wholesaler groundnut foods contained the highest mean aflatoxin levels of 0.088ppb (p= 0.27). Growing high polyamine containing crops, routine testing of aflatoxin prone foods and sensitizing food value chain players are important aflatoxin control strategies.