Contamination of pistachio fruit with aflatoxin is one of the most important problems that threaten pistachio exportation and food safety. Aflatoxin is one of the products of secondary metabolites in some toxigenc fungi - i.e. Aspergillus flavus and A. parasiticus. Early splitting and cracks on pistachio hull are one of the most important factors that lead to contamination of yield to aflatoxin in the orchard. The most important factors that may be affecting early splitting and cracks on pistachio hull are the type of the cultivar and the rootstock. This study was conducted to determine the effects of different rootstocks and scions on aflatoxin production in no.2 Pistachio Research station of Rafsanjan for 2.5 years. The experiment was a split-plot in a randomized complete block design with four rootstocks Pistacia vera cv Badami-e-Riz (Ahli), P. vera var Sarakhs (Sarakhs), P. atlantica subsp. mutica (Mutica) and P. atlantica subsp. atlantica (Atlantica) as sub-factor and three scions (Ohadi, Kalleh-Ghuchi and Ahmadaghaei) as main factor, replicated four times. Samplings were done on early split pistachios with soft and smooth hulls, shriveled and dry hulls, and irregular cracked pistachios with soft and smooth hulls, shriveled and dry hulls. Among the scions, the number of fruits per cluster was the highest in Ohadi. The percentages of early splitted pistachios with either soft and smooth hulls or shriveled and dry hulls were higher in Baneh and Atlantica rootstocks than in Ahli. The percentage of early splitting in Ahli scion was lower than Kalleh-Ghuchi scion. The percentage of cracks on pistachio hull in grafted scions on Ahli rootstock was the lowest, but showed no significant differences with other rootstocks. Kalleh-Ghuchi scion showed the lowest percentage of cracks on pistachio hull.