Chilling is an environmental factor that limits the growth and yield of agricultural productions. This research was conducted to investigate the impacts of chilling on physiological and biochemical indices in rootstocks and interspecific hybrids of pistachio and screening of tolerant rootstocks. The factors included six rootstocks (Badami-Riz-e-Zarand, Ghazvini, Sarakhs and interspecific hybrids Integerrima × Badami-Riz-e-Zarand, Integerrima × Ghazvini and Integerrima × Sarakhs) and four temperature regimes (4, 0, -2 and -4 °C) With three repetitions. Seedlings were placed in cold temperatures at the 6th to 8th stage of foliation, and cold treatments were applied to them for two hours. According to results showed the least protein content and the most ionic leakage, MDA, soluble carbohydrate, proline, total phenol, antioxidant capacity and protease activity were obtained under -4 °C. The most soluble carbohydrate, proline, total phenol, antioxidant capacity and total protein content were observed in Integerrima × Ghazvini hybrid, Ghazvini, Integerrima × Sarakhs hybrid and Sarakhs. Furthermore, the high ionic leakage and MDA in Integerrima × Badami-Riz-e-Zarand hybrid were an indicate of damage severity. In addition, Integerrima × Ghazvini, Ghazvini, Integerrima × Sarakhs and Sarakhs were identified as the most tolerant rootstocks and Integerrima × Badami-Riz-e-Zarand hybrid as the most sensitive rootstock.