Abstract Background: Aflatoxins are important and frequent teratogens, mutagens and carcinogens of maize, and the germ of the maize seed has linoleic acid, which can control aflatoxins. An aflatoxin analysis of maize flours with and without germ can show the role of the germ in the plant control of these toxins. Methods: The samples were cooked with the traditional nixtamalization process with varying calcium hydroxide content (from 0 to 2.1 w/w of corn) and steeping times of 0 and 9 h. The aflatoxin purification was performed with immunoaffinity columns, and the quantification was performed using HPLC. Results: It was found that the presence of the germ and the concentrations of 1.4 and 2.1% w/w of Ca(OH)2 had significant effects (p ≤ 0.05) on the decrease in the AFB1 and AFG1 content. Conclusion: The linoleic acid of the germ inhibited AFB1 and AFG1. However, the aflatoxin content of the experimental samples was higher than 12 μg kg-1, which is the tolerance limit permitted by NOM-247-SSA1-2008.