Diabetes is a systemic disease that affects microvasculature in almost all organs. Uterus and the ovaries may also be a target for diabetes. We investigated effects of diabetes on the uterus and the ovaries and the role of silymarin treatment on the effects of diabetes on uterine and ovarian microenvironment in a diabetic rat model. Seven non-diabetic (control) and fourteen diabetic female mature Sprague-Dawley albino rats were used. Diabetes was induced by intraperitoneal injection of 60 mg/kg streptozotocin and 100 mg/kg oral silymarin and was administered for four weeks to 7 of diabetic rats. After the treatment, blood samples were collected; hysterectomy with bilateral oophorectomy was performed for histopathological examination. Stromal degeneration, follicular degeneration, stromal fibrosis scores of the ovary and gland degeneration and stromal fibrosis scores of endometrium were significantly decreased after silymarin treatment. Silymarin treatment significantly decreased plasma TGF-beta levels and increased plasma AMH (Anti-Mullerian hormone) levels with respect to saline-treated group. This study suggests that silymarin ameliorates the uterine and ovarian damage in a diabetic rat model.