Designation of a rare 'orphan' disease is usually conferred by a prevalence of one in 1,500 to 2,500 individuals. Increasingly, orphan diseases are also being defined by their molecular fingerprints. Rare diseases are uniquely challenging from a therapeutic standpoint; it is critical to modify clinical study design of treatments for orphan disorders as well as for the increasingly smaller molecular subsets within frequently occurring cancers. In spite of the immense challenges associated with developing a treatment for a rare disorder, some of the most groundbreaking therapeutic discoveries have been made in orphan malignancies. This situation may be because a limited number of driver molecular aberrations occur in rare disorders, which can be targeted by agents. Here, we describe drug-class examples of targeted therapies for orphan diseases, with particular emphasis on malignancies or tumour-prone nonmalignant conditions, as well as potential therapeutic strategies that can be adopted to treat these orphan conditions.