The frequency of sister chromatid exchange (SCE) in patients with gastric cancer is significantly higher than that in normal individuals; however, their characteristics have not been studied. In present study, we analyzed the correlation between the cytogenetic instability of gastric cancer patients’ peripheral lymphocytes with or without hypoxia and the characteristics of gastric cancer patients. The primary lymphocyte cultures obtained from blood samples of 40 healthy donors and 69 patients with gastric cancer were examined using SCE. The average of SCE frequency in gastric cancer was 5.91 ± 2.03/cell and the SCE phenotype was not associated with gender, tumor grade, Lauren classification, and H.pylori infection. Hypoxia increased the SCE frequency as compared with normoxia, in both the control and gastric cancer lymphocyte cultures (P < 0.001). The hypoxic effect in gastric cancer was not associated with gender, tumor grade, Lauren classification, and H.pylori infection. In conclusion, hypoxia did not facilitate an increase of SCE in the lymphocytes of the gastric cancer.