Our understanding of the genetic basis of gynaecologic cancer has increased. Still this is a major cause of death. Based on a review of the literature, we present molecular diagnostic tools no available for the prevention and characterisation of cancers in the ovaries, uterus and cervix.The presentation is based on a limited literature search in PubMed, Medline, Cochrane, internet addresses for treatment protocols, and our own experiences.The cause of endometrial and ovarian cancer is mainly unknown. Around 5% of the cases are caused by inherited mutations in the BRCA1, BRCA2 or DNA repair genes. Special follow up is recommended for carriers of these mutations. Human papillomavirus (HPV) is the main cause of cervical cancer. Determination of the HPV type can contribute to a diagnosis, but it is not part of the screening programme. A more precise molecular diagnosis in endometrial and ovarian cancer can lead to development of new targeted therapy and tests for prediction of treatment response. Preliminary studies have given promising results, including studies of papillomavirus vaccines.Detection of susceptibility genes, oncogenic viruses and prognostic markers are now useful tools in the prevention, diagnosis and treatment of gynaecologic cancer. Studies of the molecular tumour profile have shown promise for the development of new treatment strategies.