Gastric cancer is the most common cancer among men in Korea, and dietary factors are closely associated with gastric cancer risk. We performed a case-control study using 334 cases and 334 matched controls aged 35-75 years. Significant associations were observed in total dietary flavonoids and their subclasses, with the exception of anthocyanidins and isoflavones (OR (95% CI): 0.49 (0.31-0.76), p trend = 0.007 for total flavonoids). However, these associations were not significant after further adjustment for fruits and vegetable consumption (OR (95% CI): 0.62 (0.36-1.09), p trend = 0.458 for total flavonoids). Total flavonoids and their subclasses, except for isoflavones, were significantly associated with a reduced risk gastric cancer in women (OR (95% CI): 0.33 (0.15-0.73), p trend = 0.001 for total flavonoids) but not in men (OR (95% CI): 0.70 (0.39-1.24), p trend = 0.393 for total flavonoids). A significant inverse association with gastric cancer risk was observed in flavones, even after additional adjustment for fruits and vegetable consumption in women. No significantly different effects of flavonoids were observed between H. pylori-positive and negative subjects. In conclusion, dietary flavonoids were inversely associated with gastric cancer risk, and these protective effects of dietary flavonoids were prominent in women. No clear differences were observed in the subgroup analysis of H. pylori and smoking status.