Ovarian cancer carries the worst prognosis among all gynecological cancers, mainly due to resistance to chemotherapy and the lack of effective screening methods for early stage detection of the disease. Early detection is necessary to reduce the mortality of ovarian cancer. Imaging techniques including transvaginal ultrasound evaluation have not reached this aim and, therefore, novel biomarkers in addition to the well established CA-125 may serve as early detection markers. Over the past years molecular screening methods and challenging biostatistical algorithms have been developed which have identified many novel biomarkers. Thus it is becoming possible to analyze the relevance of combinations of markers for identification of early stages and therapy resistance. Furthermore overcoming chemoresistance of ovarian cancer seems to be achievable by the development of targeted therapies based on the identification of certain drugs for specific targets. With molecular methods disseminated tumor cells with the potential to metastasize can also be detected in blood and bone marrow. This review gives a summary of molecular screening methods which have led to identification of novel molecular markers or are already the basis of clinical diagnostics and therapy of ovarian cancer.