BACKGROUND AND OBJECTIVE: Different menopausal manifestations may be due to low level of sex hormones. Considering the important side effects of hormone replacement therapy (HRT) provides more attention to the other modalities of treatment like phytoestrogens. So, this study was done to compare the therapeutic effect of soy protein with hormone therapy in decreasing of menopausal manifestations. METHODS: In this trial, 73 women, recently entered to menopausal state was studied in three groups for 4 months. The first group was 20 women, who underwent HRT. The second and third groups, each one including 24 & 29 women respectively, were treated by 60 gr and 100gr of soya per day. Some of the menopausal manifestations, consisting: sleep disorder, hot flush, recent memory loss, vaginal mucosal maturation index (MI), dysparonia and mean arterial blood Pressure was evaluated before and after treatment. FINDINGS: Four and nine patients from second and third group have respectively dropped out of study due to discontinuation of therapy. After therapy, hot flush improved 55%, 60% and 65% in HRT, soya 60 gr and soya 100 gr groups, respectively. Also sleep disorder improved by 40%, 50%, and 60% at the same groups, respectively. Increasing memory was seen by 60%, 40% and 65% in first, second and third groups. Vaginal MI improved 90% in first, 80% in second and 55% in third groups. Dysparonia decreased 45%, 25% and 50% in first, second, third groups, respectively.Mean arterial pressure decreased 5.6 mmHg in HRT, 1.3 mmHg in soya 60gr and 2.4 mmhg in soya 100gr groups. All findings were significant after therapy by all modalities (p<0.05). But there was no significant difference between different modalities of treatments.CONCLUSION: The result of the study showed, soya with a little difference, like HRT could improve menopausal symptoms, and its effect increases dose dependently. So considering the HRT dangers, soybeans could be a suitable treatment substitute for relief of menopausal symptoms.