To elucidate the effect of soy isoflavone supplementation on bone mineral density and antioxidant enzyme activity in 60 postmenopausal women residing in Iksan area were recruited. There were 31 participants in the treatment group and 29 in the control group. The treatment group consumed isoflavone extract capsules daily (which contained 90 mg of soy isoflavones) for 12 weeks. The study compared before and after isoflavone intake in the following areas. Physical examination, diet survey, bone mineral density (BMD) and antioxidant enzyme activity (superoxide dismutase (SOD), glutathione peroxidase (GPx), catalase (CAT) and total antioxidant capacity (TA)). The average age of the treatment group was 64.6 years and that of the control group was 66.5 years. There were no significant differences between the two groups in terms of height, weight and body mass index. Both groups maintained a regular diet pattern in terms of their average daily nutrient intake. There were no significant differences between the treatment group (23.3 mg) and the control group (24.0 mg) in terms of daily isoflavone intake based on diet. Isoflavone supplementation of 12 weeks did not resulted in any significant changes in BMD or parameters of antioxidant enzyme activity, implying the necessity of more intensive intervention for a substantial change. In conclusion, this study revealed that antioxidant enzyme activity holds a significant relationship with the bone mineral density in postmenopausal women and further systematic research on dose and period of isoflavone supplementation is needed to clearify the positive effect of isoflavone on BMD and/or blood antioxidant capacity in postmenopausal women.