In this study, the effect of mild infrared heating on total count and aflatoxins reduction of four different Iranian pistachio kernels (Ahmad Aghaei, Akbari, Fandoghi and Kaleghouchi) studied. According to previous studies, new conditions of mild infrared heating (50 – 70 °C for maximum 10.5 min) for different pistachio kernels used. Total count and aflatoxins tests done before and after the process on different naturally contaminated pistachio kernels. The results were analyzed by t-test at 5% confidence level. It shown that more than 90% of Total aflatoxin and 97-99% of B1 aflatoxin reduced in different varieties. Besides, the total count, mold and yeast numbers of the samples were decreased up to 99.96- 99.99%. This research has shown that infrared mild heating can consider as an effective method for pistachio nut and probably other nuts pasteurization and aflatoxin detoxification in a green method.