The evaluation of physiological and biochemical aspects is essential to identify clues that can assist breeders in selecting Persian walnut genotypes with considerable tolerance to drought stress. This objective can be obtained by analyzing seed biochemical compounds from different genetic resources, e.g. seeds from individual trees that are commonly exposed to drought stress. In the current research, we evaluated the effects of drought stress, as induced by PEG(6000), on the germination of walnut seeds collected from six promising genotypes (i.e. 'SS2', 'TT2', 'TT1', 'ZM1', 'Haward' and 'Chandler'). A photoperiod of 12 h was provided during the experiments, along with an average temperature of 25 +/- 1 degrees C. According to the different indexes of germination, a greater tolerance was observed among three genotypes, namely, 'ZM1', 'Haward' and 'Chandler'. In response to drought stress, the contents of proline and total soluble sugars increased, especially at intense levels of stress, whereas the amount of starch decreased. The levels of antioxidant activity significantly increased by POD, APX, CAT, SOD and LOX enzymes in the radicle and plumule tissues as the water potential reached -1.5 MPa. Three genotypes, namely, TT2', 'TT1' and 'SS2' were susceptible to cell wall damage (i.e. by lipid peroxidation). High levels of Spd and Spm in tolerant genotypes were accompanied by significant increases in the zeatin, endogenous IAA, zeatin riboside and ABA in the seeds. Our results suggest that, under drought stress, seed germination in walnuts can benefit from the accumulation of free Spd in seeds during the phases of germination. However, the accumulation of free Put appeared to be an inhibitory factor which suppressed the germination of walnut seeds.