Background: Phytoestrogens may be an alternative therapy in control of menopausal symptoms but their definite effects on breast tissue must be determined. Our study aimed to define the clinical and ultrasonographic changes of the breast after use of soy isoflavones in menopausal women. Materials and Methods: Menopausal women with hot flashes were randomly grouped as cases and controls and cases received soy isoflavones for 12 weeks. Breast examination (BE) and ultrasonography (US) were done at 0, 6 and 12 weeks. Tenderness and nodularity on BE were graded 1-4 by breast surgeons. Results: There were 30 women in the case and 26 in the control group. The mean age was 51.3 years and the mean age of menopause was 49.2 years. There was no change in the BE and US at 6 weeks in controls. In the case group, 10% had grade 1 tenderness and 13.3% grade 2 tenderness and grade 1 nodularity in BE accompanied with diffuse small cysts in US. At 12 weeks, there was no change in BE and US in the 2 groups. Conclusions: There was no statistically significant difference in the BE of the 2 groups at 6 and 12 weeks (p value=0.36 and 0.41 for nodularity and tenderness respectively) and in the US results. Although the literature contains many facts concerning PEs and the breast, further prospective studies are needed to identify structural breast changes produced by PEs in order to identify the appropriate dosage and indications of use.