OBJECTIVES Incentives are offered to pharmaceutical companies in order to increase the number of treatments for patients with rare diseases. As a consequence, a number of new drugs have been introduced on the market—drugs that often fail to meet traditional cost-effectiveness criteria. This study aims to investigate if there are societal preferences for treating patients with rare diseases differently in priority setting situations compared with common diseases. Moreover, psychological mechanisms that potentially could explain such preferences are explored. METHODS A postal questionnaire in three versions was sent out to a representative sample of the general Swedish population. Respondents were asked to choose to give treatment to a patient with a rare or a common disease in eight different scenarios. Rarity of the disease, different alternative costs, and group/individual level decisions was investigated. Psychological aspects in the presented scenaros that varied between subjects was related to proportion dominance, the identifiability of the patient, pseudo-inefficacy and if the scenario was expressed in priority or rationing terms.  RESULTS Response rate was 41 % (n= 1239). For equal cost scenarios, 42.3 % were indifferent between the rare and the common group, 23.9 % chose to prioritize the rare disease and 33.4 % the common disease. When questions were framed to be on an individul as opposed to a group level repondents were significantly (p<.001) more likely to be indifferent. Proportion dominance increased individuals’ preferences to prioritize rare diseases (p<.001). Identifiability and pseudo-inefficacy had no major effect on respondents’ choices.  CONCLUSIONS All else equal we see no strong support that a societal preference for rarity exists. However, we observe psychological effects influencing the judgments individuals make when setting priorities related to rare diseases. Whether or not these should be viewed as biases or an expression of true preferences is a matter for further discussion.