Finding new applications for existing pharmaceuticals, known as drug repositioning, is a validated strategy for resolving the problem of high expenditure but low productivity in drug discovery. Currently, the prevalent computational methods for drug repositioning are focused mainly on the similarity or relevance between known drugs based on their "features", including chemical structure, side effects, gene expression profile, and/or chemical-protein interactome. However, such drug-oriented methods may constrain the newly predicted functions to the pharmacological functional space of the existing drugs. Clinically, many drugs have been found to bind "off-target" (i.e. to receptors other than their primary targets), which can lead to undesirable effects. In this study, which integrates known drug target information, we propose a disease-oriented strategy for evaluating the relationship between drugs and disease based on their pathway profile. The basic hypothesis of this method is that drugs exerting a therapeutic effect may not only directly target the disease-related proteins but also modulate the pathways involved in the pathological process. Upon testing eight of the global best-selling drugs in 2010 (each with more than three targets), the FDA (Food and Drug Administration, USA)-approved therapeutic function of each was included in the top 10 predicted indications. On average, 60% of predicted results made using our method are proved by literature. This approach could be used to complement existing methods and may provide a new perspective in drug repositioning and side effect evaluation. Drug discovery is a time-consuming and laborious process. To bring a single de novo drug to the market, an average of more than $800 million is spent in a time period of ~15 years [1]. Moreover, about 90% of drugs fail during development in phase I clinical trials [2], a rate caused mainly by findings of low therapeutic efficacy and/or unacceptable toxicity [3,4]. Others are discovered to have similar drawbacks, even after approval by drug regulatory authorities (e.g. the US Federal Drug Administration (FDA)), or postmarketing. In exceptional circumstances, it is necessary to either modify the drug or even withdraw it from the market. The "thalidomide affair", a highly recognizable example of a drug having tragic unintended effects, is a typical example. Thalidomide was withdrawn from the market in the early 1960s because of teratogenic effects. However, it has since been reborn as an FDA-approved treatment for cancers and lepriasis owing to the discovery of new indications, namely immunomodulatory and anti-angiogenic activities [5][6][7][8].Despite enormous increases in novel technologies over recent times, the productivity of drug discovery efforts has actually decreased since the mid-1990s [9]. The need to define a novel strategy and/or utilize new resources in drug discovery is urgent. Drug repositioning, which aims to discover new indications for existing drugs, can shorten the development cycle and reduce the risk of u...