In a controlled, randomized study, we evaluated the effectiveness of various hormonal regimens in treating 70 women (mean age 34.7 ± 5.7 years) who had unilateral or bilateral ovarian cysts presumed to be physiological (functional) and a history of endometriosis. The patients were assigned randomly to one of the following groups: group I (control), no treatment; group II, oral contraceptives (35 μg ethinyl oestradiol and 1 mg norethindrone); group III, oral contraceptives (50 μg ethinyl oestradiol and 1 mg norethindrone); group IV, danazol 800 mg/day. Serum CA-125 concentrations were measured in 32 women. All medications were taken continuously for 6 weeks. Subjects were re-evaluated by pelvic examination and transvaginal ultrasound. Those with persistent cysts were offered diagnostic and possible operative laparoscopy. As 11 patients did not complete the study and five did not follow-up, the final study population comprised 54 women. At 6 weeks follow-up, complete resolution of cysts was found in: group I, 12 out of 18 (66.7%); group II, five out of nine (55.6%); group III, eight out of 14 (57.1%); and group IV, seven out of 13 (53.9%). Two of the 22 women with persistent cysts opted for 6 weeks further medical therapy and achieved complete resolution; 19 underwent laparoscopy, and one was lost to follow-up. All laparoscopic findings revealed benign masses. We found no statistically significant effect when hormonal treatment was compared with expectant management There was no correlation between serum CA-125 concentrations and the persistence or resolution of cysts.