Methods of using phytoestrogens, in particular, isoflavones in the prevention and treatment of endometriosis and related disease conditions in females. One method comprises administering a therapeutically effective dosage of a phytoestrogen to females with endometriosis, females having symptoms related to endometriosis, or to females at risk of developing or suffering recurrence of endometriosis. In another method, at least one phytoestrogen may be administered singly or in combination with at least one hormonal therapeutic agent such as GnRH analogs, androgens, progestins, estrogens or any combination thereof. The therapeutically effective dosage of the phytoestrogen or the combination therapeutic ranges between about 25 and about 250 mg/day.