Preferences among people for health system goals are important determinants in developing health policy. The aim of this study was to determine preferences for health system goals and their associations with sociodemographic characteristics in Japan. Participants were randomly selected from the general population in 5 prefectures and were asked to rank 5 health system goals in order of preference: health, health inequality, responsiveness, responsiveness inequality, and fair financing. Associations between sociodemographic characteristics and preferences for health system goals were examined using multinomial logistic regression analysis. A total of 4936 persons responded to this study. Health system goals in order of preference were health inequality (37.6%), responsiveness inequality (20.9%), health (18.4%), responsiveness (16.0%), and fair financing (7.1%). Sociodemographic characteristics such as gender, age, family status, education completed, and usage of health care services were associated with the preferred health system goal. Health policy makers should take these associations into account when developing prospective policy.