This study was designed to examine the effect of aqueous extract of Crocus sativus stigmas (CSE) and crocin (trans-crocin 4) on methyl methanesulfonate (MMS)-induced DNA damage in multiple mice organs using comet assay. Adult male NMRI mice in different groups were treated with either physiological saline (10 mL=Kg, intraperitoneal [ip]), CSE (80 mg=Kg, ip), crocin (400 mg=Kg, ip), MMS (120 mg=Kg, ip), and CSE (5, 20, and 80 mg=Kg, ip) 45 min prior to MMS administration or crocin (50, 200, and 400 mg=Kg, ip) 45 min prior to MMS administration. Mice were scarified about 3 h after each different treatment, and the alkaline comet assay was used to evaluate the effect of these compounds on DNA damage in different mice organs. The percent of DNA in the comet tail (% tail DNA) was measured. A significant increase in the % tail DNA was seen in nuclei of different organs of MMS-treated mice. In control groups, no significant difference was found in the % tail DNA between CSE-or crocin-pretreated and saline-pretreated mice. The MMS-induced DNA damage in CSEpretreated mice (80 mg=Kg) was decreased between 2.67-fold (kidney) and 4.48-fold (lung) compared to those of MMS-treated animals alone ( p < 0.001). This suppression of DNA damage by CSE was found to be depended on the dose, which pretreatment with CSE (5 mg=Kg) only reduced DNA damage by 6.97%, 6.57%, 7.27%, and 9.90% in liver, lung, kidney, and spleen, respectively ( p > 0.05 as compared with MMS-treated group). In the same way, crocin also significantly decreased DNA damage by MMS (between 4.69-fold for liver and 6.55-fold for spleen, 400 mg=Kg), in a dose-dependent manner. These data indicate that there is a genoprotective property in CSE and crocin, as revealed by the comet assay, in vivo.