IMPORTANCE OF THE FIELDPost-genome drug development has been driven by the need to study biological perturbations at the molecular system level. Systems biology visualization tools can help researchers extract hidden patterns from complex and large Omics data sets, model disease molecular mechanisms, and identify drug targets and drugs with good pharmacological and toxicological profiles.AREAS COVERED IN THIS REVIEWThis review covers basic concepts in developing and applying information visualization tools to systems biology. We describe a framework and basic data representation schemes for visual data analysis in systems biology. We review major application areas of these visualization tools within drug discovery by focusing on early-stage drug discovery tasks such as disease biology modeling, target identifications and lead identification. We also show case studies and summarize our experience using visualization tools as lessons to our readers.WHAT THE READER WILL GAINThe reader will understand what visualization tools are available for diverse types of systems biology studies in drug discovery and understand how these tools can help advance drug development.TAKE HOME MESSAGEIn spite of the complexity inherent in systems biology, proper use of information visualization tools may reveal emerging properties hidden in the data and enhance chances of success for drug discovery.