The implementation of a specific policy for rare diseases in the Brazilian Unified Health System presents challenges in terms of its rationale. Recognizing the importance of rarity in the context of public health means understanding genetics as one of the dimensions of disease and accepting thatBrazilis undergoing a period of transition in health indicators. Although most rare diseases lack pharmacological treatment and genetic counseling constitutes the best strategy for their prevention, the cost of “orphan drugs” and their consequent lack of cost-effectiveness are still claimed as hurdles to the implementation of public policies in this field. Epidemiological aspects should not be used as isolated criteria for prioritization in public policies.