Abstract Corn is the main feedstock used for ethanol production in the United States. To reduce wastage and toxicity to human and animal, using aflatoxin contaminated corn in biofuel industry is thought to be rational. Yet up to three-fold of increment of the mycotoxins in the co-product have detrimental impact on animal health. It would be desirable to inactivate or to remove aflatoxins during fermentation of corn. Smectites were previously found to be highly efficient for aflatoxin B 1 adsorption in ethanol and glucose solution, two major compounds in corn fermentation solution. The primary objective of the present study was to evaluate the aflatoxin B 1 adsorption efficiency by smectites in real corn fermentation solution. The secondary objective was to identify any interfering compound that might hinder aflatoxin B 1 adsorption. Aflatoxin B 1 adsorption by smectites in fermentation solution was found to be low. A calcium smectite (3MS) had aflatoxin B 1 adsorption capacity (Q max ) of 0.22 mol kg − 1 in the fermentation solution but 0.54 mol kg − 1 in the aqueous solution. The Fourier transform infrared (FTIR) analyses indicated that some compounds from fermentation solution were adsorbed on the smectites and had irreversible bonding with the clay minerals. Those compounds competed with aflatoxin B 1 for the adsorbing sites of smectites. The major infrared bands due to interfering compounds were at ~ 1653, 1532, 1451, and 1235 cm − 1 . These bands appeared when smectites were added to either clean or aflatoxin B 1 spiked fermentation solutions. Similar spectral bands were obtained after treating the smectites with zein, a major protein in corn. Thus, the major interfering compounds in fermentation solution were believed to be proteins. The XRD results proved the adsorption of the proteins in the interlayer of smectites. After heating at 300 °C, smectites reacted with fermentation solution had d-spacing of at least 15 A, whereas the pure smectites collapsed to ~ 10 A. This reflected great interferences of the compounds, most possibly proteins on aflatoxin B 1 adsorption by the smectites. However, despite of strong interferences, adsorption experiments suggested that smectites were still able to adsorb aflatoxin B 1 to some extent. Presence of characteristic aflatoxin B 1 bands at ~ 1595, 1383, 1362, 1304, 1272, and 1205 cm − 1 on smectite complexes treated in fermentation solution revealed the existence of the mycotoxins on the clay minerals. Strategies should be taken to enhance the selectivity of smectites for the aflatoxins in corn fermentation solution.