The identification of tissue-based biomarkers is a major task for molecular cancer research. As ovarian cancer is a malignancy with a particular poor prognosis, new diagnostic tests are needed for the planning of an individualized therapy. Diagnostic biomarkers are investigated on different biological levels using genomics, transcriptomics, proteomics or metabolomics as a major approach. Protein biomarkers as well as RNA biomarkers can be measured in formalin-fixed tissue using immunohistochemistry as well as new techniques for isolation of nucleic acids. Furthermore, gene expression as well as metabolic signatures can be determined using frozen tissue. In a first evaluation, metabolomics has been used to investigate different types of ovarian tumors. In a systems pathology approach the results from the different biological levels are integrated to a combined signature that reflects the biological behaviour of the tumor.