The current pathological methods and existing serum tumor markers for gynaecologic malignancies does not provide efficient information regarding the therapeutic intervention to which a cancer responds. Cancers classified based on the molecular profile determines the abnormalities at the genetic level. This in turn has led to the discovery of cancer-specific biomarkers. The cancer-specific biomarkers are used against target specific gene products or pathways. A molecular profile includes both genetic and epigenetic signatures which are specific to a particular type of cancer. Genetic and epigenetic markers are more sensitive and specific which may be efficient in early diagnosis of cancer and aids in multiple therapeutic alternatives. In future, a combination of various biomarkers from genomics (genes, micro RNA [miRNA], mutations, Single Nucleotide Polymorphisms [SNPs]), proteomics (peptides, proteins, modifications) and metabolomics (small-molecule intermediates, hormones, systemic compounds) will provide a promising assay platform that suits specific treatment options.