Numbers of epidemiologic studies assessing soy consumption and risk of breast cancer have yielded inconsistent results. We aimed to examine the association between soy isoflavones consumption and risk of breast cancer incidence or recurrence, by conducting a meta-analysis of prospective studies. We searched for all relevant studies with a prospective design indexed in PUBMED through September 1st, 2010. Summary relative risks (RR) were calculated using fixed- or random-effects models. Pre-specified stratified analyses and dose-response analysis were also performed. We identified 4 studies of breast cancer recurrence and 14 studies of breast cancer incidence. Soy isoflavones consumption was inversely associated with risk of breast cancer incidence (RR = 0.89, 95% CI: 0.79-0.99). However, the protective effect of soy was only observed among studies conducted in Asian populations (RR = 0.76, 95% CI: 0.65-0.86) but not in Western populations (RR = 0.97, 95% CI: 0.87-1.06). Soy isoflavones intake was also inversely associated with risk of breast cancer recurrence (RR = 0.84, 95% CI: 0.70-0.99). Stratified analyses suggested that menopausal status may be an important effect modifier in these associations. We failed to identify a dose-response relationship between total isoflavones intake and risk of breast cancer incidence. Our study suggests soy isoflavones intake is associated with a significant reduced risk of breast cancer incidence in Asian populations, but not in Western populations. Further studies are warranted to confirm the finding of an inverse association of soy consumption with risk of breast cancer recurrence.