This article reviews the main prognostic and predictive biomarkers of endometrial (EC) and ovarian carcinoma (OC). In EC, prognosis still relies on conventional pathological features such as histological type and grade, as well as myometrial or lymphovascular space invasion. Estrogen receptor, p53, Ki-67, and ploidy analysis are the most promising biomarkers among a long list of molecules that have been proposed. Also, a number of putative predictive biomarkers have been proposed in molecular targeted therapy. In OC, prognosis is predominantly dependent on disease stage at diagnosis and the extent of residual disease at primary operation. Diagnostic markers which aid in establishing histological type in OC are available. However, not a single universally accepted predictive or prognostic marker exists to date. Targeted therapy has been growingly focused at in recent years, in view of the frequent development of chemoresistance at recurrent disease. The present review emphasizes the crucial role of correct pathological classification and stringent selection criteria of the material studied as basis for any evaluation of biological markers. It further emphasizes the promise of targeted therapy in EC and OC, while simultaneously highlighting the difficulties remaining before this can become standard of care.