Seeds of Zea mays L. were exposed to allatoxine B1 (AFB1), aflatoxine G1 (AFG1) and selenium (Se) alone and in combination and allowed to germinate. Phytohormone levels of GA-like substances (GAs), trans-Zeatin (t-Z) and Indole-3-acetic acid (IAA) were determined by High Performance Liquid Chromatography (HPLC) when the roots of the germinating seeds reach 1.5-3.0 cm in length. The levels of endogenous hormones decreased in seeds treated with AFB1 and AFG1 compared to control; however an increase was noted in seeds exposed to AFG1 and Se together. AFB1 and Se treatment caused reduced hormone levels in most of the treatments. When plants were exposed to Se alone, the highest levels of GAs, t-Z and IAA were observed in the application of 800 ppm Se. The highest levels of GAs, t-Z and IAA were observed when seeds were treated with 0.2 ppm AFG1 + 8 ppm Se, 0.2 ppm AFG1 + 8 ppm Se and 0.2 ppm AFG1 + 0.08 ppm Se, respectively, whereas the lowest levels of the hormones were observed in 0.2 ppm AFB1 + 8 ppm Se, 0.2 ppm AFB1 + 0.08 ppm Se and 0.1 ppm AFB1, respectively. In conclusion, the levels of phytohormones were reduced by the treatment of AFB1 and AFG1 alone. However Se removed the negative effect of AFB1 on phytohormones, but not AFB1.