Many studies have shown that soybean and isoflavones have a favorable effect on bone mass for postmenopausal women, but few data are available on young Asian women. To investigate the effect of soybean and isoflavone intake on bone mineral density (BMD) and its change among young Korean women over 2 years, we conducted a longitudinal study for 34 women. The BMD was measured 3 times with 1-year intervals by dual x-ray absorptiometry at the lumbar spine and femur (neck, Ward's triangle [WT], and trochanter). Dietary intake was assessed up to 8 times by 24-hour recall with average 4-month interval. During the study period, BMD increased significantly for lumber spine and WT (2.5% and 5.2%). The average daily intake of soybeans and isoflavones was 39 g and 8 mg, respectively. Soybean intake and total isoflavone intake had positive correlation on femoral neck (FN) and WT. By longitudinal mixed-model regression analysis, BMD increased 0.26% per 1 mg of isoflavone intake per year in the FN and 0.31% for WT (P = .05 and .008). In conclusion, soybean and isoflavone intake have a positive effect on the change of BMD on the FN and WT among young Korean women. Because soybean and isoflavone intakes could be confounded by other nutrients, the positive effects of isoflavones on bone should be further investigated.