To determine the nature and surgical management of ovarian cysts. Retrospective case-note study. Large Childrens' Hospital: Alder Hey NHS Foundation Trust. Children undergoing surgery for ovarian cysts between 1991 and 2007. Cases identified using coding and the pathology database, and analysed using snap 9. Extent of surgery performed. Size and histological features of cysts removed. A total of 155 cases were identified. There were 62 ovarian cysts in children under nine who were prepubertal. There were 58 neoplastic cysts in total. Most were benign teratomas (36). Ten cysts were malignant, including five granulosa cell tumours, one yolk sac tumour, one endodermal sinus tumour and one dysgerminoma. Tumour markers were performed in only 16 cases (10%). Sixty-one (39%) had an ultrasound scan and 16 (10%) had a computed tomography (CT) or magnetic resonance imaging (MRI) scan. Ninety girls (58%) had an oophorectomy and 40 (25%) had an ovarian cystectomy. Oophorectomies were performed for all cases of malignancy, but 75 were also performed for benign or normal pathology. Only 16% of cases were referred to the paediatric gynaecologist and all were for post-operative management. We recommend the greater use of imaging of the pelvis and tumour markers preoperatively. There should be greater use of conservative expectant management or ovarian-sparing surgery in view of the low risk of malignancy in this age group. The practice of removing ovaries for benign cysts may be overcome by appointing more gynaecologists with advanced training skills training in paediatric and adolescent gynaecology.