Rare diseases are defined as conditions with a prevalence of less than 1/2,000. To date between 6,000 and 7,000 rare diseases have been identified and many of those have manifestations that include intellectual disability, developmental disorders or other behavioural phenotypes. In this special issue we bring together a range of papers where rare diseases were used as models to delineate specific aspects of learning and memory, or behaviour. In this introductory paper we summarize some of the lessons we can learn from rare diseases. Firstly, we learn that, collectively, rare diseases are not at all rare. As many as 1 in 20 individuals may be affected by a rare disease at some point in their life. Secondly, we learn that rare diseases may share common pathophysiological mechanisms. A discovery in one can therefore have direct relevance to many others. A third lesson is that the study of rare diseases can lead to an understanding of common disorders, as exemplified by the relationship between Trisomy 21 (Down syndrome) and Alzheimer's disease. A fourth lesson from rare diseases is that the 'one gene-one functional consequence' assumption is not correct. Finally, rare diseases have shed new light on the strengths and weaknesses of animal models in the study of behavioural phenotypes.