This study aimed to compare AFM1 occurrence in different cheese types produced by organic and conventional systems; and to evaluate the risk of food exposure to AFM1. A total of 176 commercial cheeses of 17 types were analyzed, 84 of organic and 92 of conventional production. Determination of AFM1 was performed by high- performance liquid chromatography (HPLC), being detected in 30.5% of samples, with 4.8% of organic cheese samples presenting quantifiable AFM1 values between 0.88 and 1.50 μg/kg. On the other hand, 4.3% of conventional cheese samples with values between 0.79 and 6.70 μg/kg. Two conventional cheese samples were above the limit of AFM1 allowed for cheeses by the Brazilian legislation. No statistical difference were found between organic and conventional cheeses regarding the occurrence (p = 0.1780) and concentration of AFM1 (p = 0.1810), according to the Chi-square and the T test, respectively. Estimated daily intake (EDI) and hazard index (HI) of dietary exposure to AFM1 were 0.26 ng/kg/day and 1.28 ng/kg/day, respectively, for conventional cheese samples, and 0.09 ng/kg/day and 0.47 ng/kg/day for organic samples, with no statistical difference for EDI (p = 0.1729) and HI (p = 0.1802) between the two production systems. Comparison between several cheese types from conventional and organic systems indicated that AFM1 is an obstacle to dairy production. Control and prevention of AFM1 contamination, as well as detoxification methods in the final products, are necessary. In the case of organic products, additional research is needed in order to determine which control and detoxification methods should be allowed in this production system.