Cellular life can be represented and studied as the ‘interactome’ - a dynamic network of biochemical reactions and signaling interactions between active proteins. Systemic networks analysis can be used for the integration and functional interpretation of high-throughput experimental data, which are abundant in drug discovery but currently poorly utilized. The composition and topology of complex networks are closely associated with vital cellular functions, which have important implications for life science research. Here we outline recent advances in the field, available tools and applications of network analysis in drug discovery.