OBJECTIVE: To examine the patient perspective on the risks and benefits of linking existing data sources for research. MATERIALS AND METHODS: Between December 2015 and February 2016, we fielded a questionnaire in PatientsLikeMe, an online patient community representing over 2500 health conditions. The questionnaire was developed using subject matter expertise and patient feedback from a concept elicitation phase (N = 57 patients). The final questionnaire consisted of 37 items. RESULTS: Of n = 5741 who opened the email invitation, n = 3516 respondents completed the questionnaire (61.2%). Of these, 73.8% were women, 86.4% were Caucasian, 14.5% were 65 or older, and 44.9% had completed college or post-graduate education. Questionnaire respondents indicated that the most important benefits of sharing data were "helping my doctor make better decisions about my health" (94%) and "helping make new therapies available faster" (94%). The most important data sharing risk identified was health data being "stolen by hackers" (87%). Of 693 patients who were not comfortable with researchers accessing their de-identified data, most reported that their comfort levels would increase if they were able to learn how their data was protected (84%). In general, responders felt more comfortable when unique identifiers such as social security number (90%) and insurance ID (82%) were removed from the data for linkage and research use. DISCUSSION: The majority of patients in a US-based online community are comfortable with researchers accessing their de-identified data for research purposes. CONCLUSIONS: Developing methods to link databases minimizing the exposure of unique identifiers may improve patient comfort levels with linking data for research purposes.