Genetic profiling of cancer may lead to a better understanding of its intra- as well as intertumoural heterogeneity as well as targeted, patient-oriented cancer therapy. Due to the recent advances in molecular biology, important steps towards this goal have been accomplished. Among others, several large profiling analyses of gynaecologic malignancies have been completed and published recently. Most notably, these comprehensive molecular analyses expose a high degree of cancer complexity and heterogeneity. Integration of this data into clinical practice will result in new tumour classifications and possibly change our understanding of cancer pathogenesis and thus necessitate the development of novel diagnostic and therapeutic algorithms.