Low drug productivity has been a significant problem of the pharmaceutical industry for several decades even though numerous novel technologies were introduced during this period. Currently pharmacologic dogma, "single drug, single target, single disease", is at the root of the lack of drug productivity. From a systems biology viewpoint, network pharmacology has been proposed to complement the established guiding pharmacologic approaches. The rationale for network pharmacology as a major component of drug discovery and development is that a disease can be caused by perturbation of the disease-causing network and a drug may be designed to interact with multiple targets for modulation of such a network from the disease status toward normal status. Therefore, network pharmacology has been applied to guide and assist in drug repositioning. Drugs exerting their therapeutic effects may directly target disease-associated proteins, but they may also modulate the pathways involved in the pathological process. In this review, we discuss the progresses and prospects in network pharmacology, focusing on drug off-targets discovery, disease-associated protein identification, and pathway analysis for elucidating relationships between drug targets and disease-associated proteins.