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Aflatoxin contamination of maize in Rwanda and underlying causes are poorly documented. This study aimed to address this gap where maize samples for aflatoxins analysis were collected from two different agro-ecological zones and the temperature and relative humidity conditions during the time preceding sample collection were monitored to determine the conditions conducive to this contamination. Maize was analysed for moisture content and aflatoxin contamination and the temperature and humidity data were used to estimate the saturation deficit of the ambient air as an indicator of risk of contamination, which is high when the saturation deficit is low. Results showed an average lower saturation deficit of 0.0018 kg H₂O kg−1 in the high-altitude Volcanic region compared to the 0.00095 kg H₂O kg−1 recorded in the lower altitude region of the Eastern Savannah. Given the high moisture content in most of the analysed samples, this meant that it is more challenging to dry maize to the safe storage moisture content in the Volcanic region compared to the Eastern Savannah. The mean aflatoxin contamination was 40.45 μg kg−1 in the Volcanic region significantly higher than 4.66 μg kg−1 in the Eastern Savannah. Aflatoxin G1 was predominant among the contaminated samples. Affordable drying technologies that use renewable sources of energy should be developed and made accessible to farmer cooperatives. • Aflatoxins contamination in maize during storage is influenced by temperature and humidity conditions. • Low temperature drying of maize relies on temperature and humidity conditions in the environment. • Saturation deficit of air can be based on to assess the suitability of air to dry maize to the desired moisture content. • Low saturation deficit means prolonged drying time and thus increased risk of contamination. [ABSTRACT FROM AUTHOR]