Cardiovascular diseases are the major cause of morbidity and mortality worldwide. Given the complex pathophysiology of cardiovascular diseases, an experimental approach capable of identifying multiple signaling networks activated in the heart upon pathological conditions could be particularly effective to identify new diagnostic, prognostic or therapeutic targets. Latest generation techniques now allow high-resolution investigations of the entire genome, the proteome and the cellular metabolome, as well as epigenetic modifications and associated gene expression profiles. In particular, the integration of epigenomic and transcriptomic data in the normal or pathological heart is a promising approach to identify novel molecular targets. These methods, although promising and innovative, can present several technical and analytical pitfalls. Here we will briefly describe these aspects and possible strategies to optimize the search for new diagnostic or therapeutic targets for cardiovascular diseases in the post-genomic era.Copyright© by Aracne Editrice, Roma, Italy.