Our previous study on bone health among premenopausal women showed that bone mass consolidation is attained by the early 30s, and small loss of spinal bone mineral density (SBMD) occurs soon after peak bone mass attainment. Recent interest has been shown in the potential beneficial effects of phytoestrogens on bone health. However, data are lacking, particularly in Asian women. This study aims to investigate the effect of soy isoflavones intake on the maintenance of peak bone mass in a cohort of 132 women aged 30-40 years who were followed up for 3 years. Baseline measurements of SBMD (L2-L4) were obtained using dual-energy X-ray densitometry, and dietary intake of soy foods and other key nutrients, including dietary calcium, were obtained through a quantitative food frequency method. Information on body measurements; physical activity (PA), weight-bearing activity in particular; age of menarche; and number of pregnancies were obtained at baseline. Repeated measurements of SBMD were obtained yearly for a further 3 years with an average follow-up time of 38 months. Analyses were performed on 116 subjects with at least three SBMD measurements (at baseline, 3-year follow-up, and at least one measurement during follow-up). The individual SBMD regression slope was computed for each of the subjects. Soy isoflavones consumption was categorized as quartiles of intake. We observed a significant difference in the SBMD individual regression slopes between women belonging to the fourth and first soy isoflavones intake quartiles. The positive effect of soy isoflavones on SBMD remained after adjusting for age and body size (height, weight, and bone area). Multiple linear regression analysis including the other known covariates (lean body mass, PA, energy adjusted calcium, and follow-up time) showed that soy isoflavones, together with these variables, accounted for 24% of the variances of the SBMD individual regression slope. This longitudinal study shows that soy intake had a significant effect on the maintenance of SBMD in women aged 30-40 years. The effects of phytoestrogens on bone health should be explored further in a population with habitual dietary soy but low calcium intake.