This study investigated the development of functional ovarian cysts during pituitary down-regulation prior to in-vitro fertilization (IVF), and identified 16 cases of cysts in 288 IVF cycles studied. Comparing the patients with functional ovarian cysts to the other 272 IVF cycles, there was no significant difference in age or incidence of endometriosis but significantly (P < 0.01) more patients with cysts had ovulatory dysfunction. The serum progesterone was < 5.7 nmol/l in all 16 patients with cysts on day 4 of the IVF cycle, and in eight of these patients the serum progesterone was < 5.7 nmol/l on the day buserelin was commenced. In 10 of the 16 patients with cysts, serum oestradiol concentrations remained elevated despite the prolonged use of buserelin, and the cysts were aspirated. The aspirate in all cases was clear without any suggestion of endometriosis. The cyst aspirates had significantly lower progesterone (P < 0.001), higher androstenedione (P < 0.01) and similar oestradiol concentrations to 10 follicular fluid samples collected at the time of oocyte retrieval. This study suggests that functional ovarian cysts may develop during pituitary down-regulation, and these cysts are follicular cysts rather than persistent corpora lutea or endometriomata.