This study was conducted to clarify the effect of ingesting soy isoflavone extracts (not soy protein or foods containing isoflavones) on bone mineral density (BMD) in menopausal women. PubMed, CENTRAL, ICHUSHI, CNKI, Wanfang Data, CQVIP, and NSTL were searched for randomized controlled trials published in English, Japanese, or Chinese reporting the effects of soy isoflavone extracts on lumbar spine or hip BMD in menopausal women. Trials were identified and reviewed for inclusion and exclusion eligibility. Data on study design, participants, interventions, and outcomes were extracted. Eleven, seven, five, and five trials were finally selected for estimation of the effects on spine, femoral neck, hip total, and trochanter BMD, respectively. Meta-analysis including data from1240 menopausal women revealed that daily ingestion of an average of 82 (47-150) mg soy isoflavones (aglycone equivalent) for 6-12 months significantly increased spine BMD by 22.25 mg/cm2 (95% CI: 7.62, 32.89; p=0.002), or by 2.38% (95% CI: 0.93, 3.83; p=0.001) compared with controls (random-effects model). Subgroup analyses indicated that the varying effects of isoflavones on spine BMD across trials might be associated with study characteristics of intervention duration (6 vs. 12 months), region of participant (Asian vs. Western), and basal BMD (normal bone mass vs. osteopenia or osteoporosis). No significant effects on femoral neck, hip total, and trochanter BMD were found. Soy isoflavone extract supplements increased lumbar spine BMD in menopausal women. Further studies are needed to address factors affecting the magnitudes of effect on spine and to verify the effect on hip.