A study was carried out to assess levels of contamination of aflatoxins and fumonisins (B1 + B2) in maize produced, stored and consumed in rural households in Malawi. A total of 9 districts were selected across the country representing 3 districts from each of the Northern, Central and Southern regions respectively. Households were selected at random in each district where 10 maize samples were collected for laboratory analysis. Aflatoxins and fumonisins were analyzed using a single step lateral flow immunochromatographic assay based on a competitive immunoassay format. The detection limit for aflatoxins was 2 μg/kg with a quantitation range of 2-150 μg/kg and that for fumonisins was 1 mg/kg with a quantitation range of 1-7 mg/kg. It was found that samples in the Southern region were highly contaminated, with the Chikhwawa district having high levels of both aflatoxins and fumonisins in maize. The Northern region had the least contamination. The maximum detected amount of aflatoxins was 140 μg/kg. The maximum detected amounts of fumonisins was 7 mg/kg. About 20% of maize samples exceeded the tolerable maximum limit for aflatoxins in Malawi. Aflatoxins and fumonisins were found to co-occur with contamination levels exceeding 100 μg/kg for both aflatoxins and fumonisins.