Introduction: The literature of orphan drugs and rare diseases between 2000 and 2014 is reviewed. The overall structure of its intellectual landscape is characterized in terms of thematic concentrations of co-cited references and emerging trends of surging keywords and citations to references through a scientometric review – a quantitative study of scientific literature.

Areas covered: The review is based on two sets of bibliographic records retrieved from the Web of Science. The core dataset, consisting of 9461 original research articles and review papers, was constructed from a topic search. The expanded dataset, consisting of 82,765 articles and reviews, was constructed by citation expansion.

Expert opinion: The study has revealed three broad categories of research. The research policy category focuses on the strategic and integral role of the study of orphan drugs and rare diseases in a wide-ranging societal context, including optimizing the allocation of resources and setting appropriate evaluation standards. The basic research category focuses on understanding the complex biological and genetic mechanisms of rare diseases. The disease-specific research category focuses on specific rare diseases with clinical and therapeutic goals. The study has revealed the fundamental role of genetic variation in linking a diverse range of rare and complex phenotypic patterns. The field would benefit from more comprehensive reviews of all three categories as a whole and disseminating findings and technical advances across various specialties. Finally, building stronger connections between the study of rare diseases and the study of more common diseases is recommended for all three categories.