Objective: The most significant consequence of the oxidative stress is thought to be the DNA modifications, which can become permanent via the formation of mutations and other types of genomic instability resulting cellular dysfunction. Serum/glucose deprivation (SGD) has served as an excellent in vitro model for the understanding of the molecular mechanisms of neuronal damage during ischemia and for the development of neuroprotective drugs against ischemia-induced brain injury. Nigella sativa and thymoquinone (TQ), its most abundant constituent, have been shown to possess anti-inflammatory, antioxidant, chemopreventive and anti-neoplastic effects both in vitro and in vivo. Materials and Methods: PC12 cells were cultured in DMEM medium containing 10% (v/v) fetal bovine serum, 100 units/ml penicillin, and 100 µg/ml streptomycin. Initially Cells were pretreated with different concentrations of N. sativa extract (10, 50, 250 µg/ml) and TQ (1, 5, 10 µg/ml) for 6 h and then deprived of serum/glucose (SGD) for 18 h. the alkaline comet was used to evaluate the effect of these compounds on DNA damage assay following ischemic insult. The percent of DNA in the comet tail (% tail DNA) was measured as an indicator of DNA damage. Results: A significant increase in the % tail DNA was seen in nuclei of cells following SGD induced (p<0.001). In control groups, no significant difference was found in the % tail DNA between NSE- or TQ-pretreated and vehicle-pretreated PC12 cells (p>0.05). NSE and TQ pretreatment resulted in a significant decrease in DNA damage following ischemic insult (p<0.001).This suppression of DNA damage by NSE and TQ was found to be depended on the dose. Conclusion: These data indicate that there is a genoprotective property in NSE and TQ, as revealed by the comet assay, under SGD condition in PC12 cells.