Intraoperative frozen sections are particularly important for ovarian tumors because definitive preoperative histology is not possible. The diagnostic accuracy of frozen sections is highest for primary invasive ovarian carcinomas and benign ovarian lesions, followed by borderline tumors and poorest for ovarian metastases and rare neoplasms, such as germ cell tumors. Endometrial carcinoma should be diagnosed preoperatively by curettage or biopsy. For endometrioid endometrial carcinomas the indications for lymphadenectomy are often based on intraoperative assessment of the uterus. The differential diagnosis of low grade stromal neoplasms is based on myometrial invasion and can be supported by assessment of frozen sections as well as the diagnosis of other mesenchymal uterine tumors suspected of being malignant. Frozen sections of pelvic lymph nodes provide the possibility of immediate subsequent para-aortic lymphadenectomy in endometrial and cervical carcinomas but have recently lost importance. Sentinel node biopsy with intraoperative frozen section analysis is routinely performed only for vulval carcinoma. The German Association of Gynecological Oncology (AGO) recommends deferred diagnosis and a two stage surgical procedure for any doubtful intraoperative ovarian histology. Intraoperative frozen sections for endometrial carcinoma and lymphadenectomy specimens as well as for sentinel node biopsies are currently not recommended but are also not completely rejected.