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Neglected and rare diseases traditionally have not been the focus of large pharmaceutical company research as biotech and academia have primarily been involved in drug discovery efforts for such diseases. This area certainly represents a new opportunity as the pharmaceutical industry investigates new markets. One approach to speed up drug discovery is to examine new uses for existing approved drugs; this is termed drug repositioning or drug repurposing and has become increasingly popular in recent years. Analysis of the literature reveals that using high-throughput screening there have been many examples of FDA approved drugs found to be active against additional targets that can be used to therapeutic advantage for repositioning for other diseases. To date there are far fewer such examples where in silico approaches have allowed for the derivation of new uses. It is suggested that with current technologies and databases of chemical compounds (drugs) and related data, as well as close integration with in vitro screening data, improved opportunities for drug repurposing will emerge. In this publication a review of the literature will highlight several proof of principle examples from areas such as finding new inhibitors for drug transporters with 3D pharmacophores and uncovering molecules active against Mycobacterium tuberculosis (Mtb) using Bayesian models of compound libraries. Research into neglected or rare/orphan diseases can likely benefit from in silico drug repositioning approaches and accelerate drug discovery for these diseases.