Drug adverse effects (ADEs) and toxicities have been extensively studied from chemical structure, genetic, biological systems and clinical perspectives. The rapid accumulation of chemical, biological and clinical data are highly useful for characterizing and predicting ADEs, and have enabled increasing exploration of computational methods as low cost tools for predicting various ADEs and toxicities. This article reviews the strategies, current progresses, underlying difficulties and future prospects in using computational methods for predicting ADEs and toxicities.