Sorting of pistachio lots could have an important role in their aflatoxin amount. In order to determine this effect in different cultivars, samples were divided into 7 categories: Yellow-brown stain, dark-grey stain, large, medium, tiny, damaged and non-split. Results showed that the amount of aflatoxins (using TLC-Scanner method) in pistachios without stains is low. The mean percent of yellow-brown stained nuts in Fandoghi, Ahmad Aghaei and Kale-Ghoochi cultivars were 4.6, 2.26 and 1.13 and the mean percent of grey-black stained nuts were 4.68, 4.60 and 1.16 respectively. The mean of aflatoxin in yellow-brown stained nuts were 136.25, 632.38 and 120.35 ng/g and in grey-black stained nuts were 28.68, 292.8, 7.28 ng/g respectively. With completely separating of stained nuts amount of aflatoxin in Fandoghi, Ahmad Aghaei and Kale-Ghoochi lots were decreased 89.52, 96.43 and 95.10 percent respectively. There were significant differences between the aflatoxin amounts of stained nuts in pistachio cultivars.