Background: Despite diverging definitions on rare conditions, people suffering from rare diseases share similar difficulties. A lack of experience by health professionals, a long wait from first symptoms to diagnosis, scarce medical and scientific knowledge, and unsatisfactory treatment options all trigger the search for health information by patients, family members, and physicians. Examining and systematically integrating stakeholder needs can help design information platforms that effectively support this search.Objective: The aim of this study was to innovate on the group decision-making process involving patients, family members, and physicians for the establishment of a national rare disease Internet platform. We determined differences in the relevance of health information—especially examining quantifiable preference weights—between these subgroups and elucidated the structure and distribution of these differences in people suffering from rare diseases, their family members, and physicians, thus providing information crucial to their collaboration.Methods: The included items were identified using a systematic Internet research and verified through a qualitative interview study. The identified major information needs included medical issues, research, social help offers, and current events. These categories further comprised sublevels of diagnosis, therapy, general disease pattern, current studies, study results, registers, psychosocial counseling, self-help, and sociolegal advice. The analytic hierarchy process was selected as the group decision-making tool. A sensitivity analysis was used to determine the stability and distribution of results. t tests were utilized to examine the results’ significance.Results: A total of 176 questionnaires were collected; we excluded some questionnaires in line with our chosen consistency level of 0.2. Ultimately, 120 patients, 24 family members, and 32 physicians participated in the study (48 men and 128 women, mean age=48 years, age range=17-87 years). Rankings and preference weights were highly heterogeneous. Global ranking positions of patients, family members, and physicians are shown in parentheses, as follows: medical issues (3/4, 4, 4), research (3/4, 2/3, 3), social help offers (1, 2/3, 2), and current events (2, 1, 1); diagnosis (6, 8, 9), therapy (5, 9, 7), general disease pattern (9, 4/5/6, 6), current studies (7, 4/5/6, 3), study results (8, 7, 8), registers (4, 1, 5), psychosocial counseling (1, 2, 4), self-help (3, 3, 2), and sociolegal advice (2, 4/5/6, 1). Differences were verified for patients for 5 information categories (P=.03), physicians for 6 information categories (P=.03), and family members for 4 information categories (P=.04).Conclusions: Our results offer a clear-cut information structure that can transparently translate group decisions into practice. Furthermore, we found different preference structures for rare disease information among patients, family members, and physicians. Some websites already address differences in comprehension between those subgroups. Similar to pharmaceutical companies, health information providers on rare diseases should also acknowledge different information needs to improve the accessibility of information.