Busia and Kisii Central districts are areas in western Kenya that have repeatedly reported high levels of stunting growth in children and an increase in hepatocellular carcinoma (HCC); an aspect often positively associated with chronic exposure to aflatoxins especially through consumption of foods such as peanuts. The objectives of the study were to determine the incidence, types and levels of aflatoxin in different varieties of peanuts produced in Busia and Kisii Central districts. One hundred and two (102) peanuts samples were collected from farmers' in each district. Aflatoxin types and levels of aflatoxins were analyzed using high performance liquid chromatography (HPLC) technique. All the peanuts samples from Kisii Central and 97.06% samples from Busia were contaminated with aflatoxins. However, aflatoxin was not detected in 2.94% of samples from Busia district. The levels of total aflatoxin ranges were 0.1 to 268 μg/kg and 1.63 to 591.1 μg/kg in peanuts from Busia and Kisii Central respectively. Majority of peanuts samples had levels within Kenya Bureau of Standards (KEBS) and European Union (EU) regulatory limits for total aflatoxins. Improved variety (Valencia red) had significantly lower aflatoxin contamination compared to local varieties (Uganda local red, Homabay local and Local red). Aflatoxins B1, B2, G1 and G2 were found in peanuts; B1 was the most predominant in both districts (t = 12.4, df = 3, P = 0.034). The levels of aflatoxins especially in peanuts from Kisii Central district were high (591.1 μg/kg) where 44.6% of samples analyzed were unfit for even animal feed (USFDA regulatory limit). An assessment on the levels of aflatoxins should be done by the relevant stakeholders in other key foods in the areas for example maize. The most lethal aflatoxin type B1 was found to be the most predominant peanuts from both districts of study. This calls for frequent aflatoxin screening of peanuts from the districts particularly aflatoxin type B.