In health economics, the valuation of health states is usually based on individual preferences and incremental cost on a per patient basis, excluding potential sources of social value beyond the satisfaction of individual (selfish) preferences. Multi-criteria decision analysis (MCDA) and social cost value analysis (SCVA) have been proposed as alternatives better capturing “other” drivers of value than gains in length and quality of life. Both MCDA and SCVA should be informed by robust empirical evidence on the social preferences of citizens covered by a health scheme. Based on a comprehensive literature review, a Swiss multi-stakeholder consensus (“SwissHTA”), and expert recommendations on valuation principles for ultra-rare disorders, we designed the Social Preferences for Health Care Interventions (“SoPHI”) Study as a discrete choice experiment (DCE) to assess the relative weights of selected attributes of health care interventions, their interaction, and the impact of the level of information on the implications of rarity and cost (potential framing effects). After cognitive and quantitative pretests, the main survey was conducted in Switzerland and enrolled 1,501 respondents, who underwent an initial preference formation phase before participating in the DCE experiment. Attributes tested were health state before and after intervention (separately for length and quality of life), age, prevalence (or “rarity”), and social health insurance premiums as the payment vehicle, which we chose to capture social preferences as “social willingness-to-pay” including risk aversion and caring externalities. The study provides support for the importance of all attributes tested, with change in remaining life expectancy, incremental cost (from a citizens’ perspective), and quality of life improvements being more relevant than prevalence and the age effect observed in the experiment. The SoPHI Study provides empirical support for the contribution to social value by all attributes tested, which contrasts with the assumptions underlying conventional cost effectiveness analyses.