Rare Diseases Epidemiology is a novel action field still largely unexplored. However, Rare Diseases is a topic of growing interest at world level. The aims of this chapter are to revise useful epidemiological tools and define areas where epidemiology can help improve the rare disease knowledge, and facilitate policy decisions taking into account the real burden of rare diseases in society. This chapter also seeks to describe: the problems of coding and classification of diseases, measuring disease frequency, the study designs and association studies, the causality, the evolution from descriptive to epigenetic epidemiology and the natural history of disease. One of the major challenges facing analytical epidemiology and clinical epidemiological research into rare diseases is that genes can be involved in both aetiology and prognosis. Despite the many similarities between genetic association studies and classic observational epidemiological studies, the former pose several specific limitations, including an unprecedented volume of new data and the likelihood of very small individual effects, as well other limitations. Selecting the appropriate pathway from among all those available, i.e. the one that best relates genes from the various known regions and disease mechanisms, is crucial for the success of this type of studies.