Background Use of the Internet to conduct randomised controlled trials is increasing, and provides potential to increase equity of access to medical research, increase the generalisability of trial results and decrease the costs involved in conducting large scale trials. Several studies have compared response rates, completeness of data, and reliability of surveys using the Internet and traditional methods, but very little is known about participants' attitudes towards Internet-based randomised trials or their experience of participating in an Internet-based trial. Objective To obtain insights into the experiences and perspectives of participants in an Internet-based randomised controlled trial, their attitudes to the use of the Internet to conduct medical research, and their intentions regarding future participation in Internet research. Methods All English speaking participants in a recently completed Internet randomised controlled trial were invited to participate in an online survey. Results 1246 invitations were emailed. 416 participants completed the survey between May and October 2009 (33% response rate). Reasons given for participating in the Internet RCT fell into 4 main areas: personal interest in the research question and outcome, ease of participation, an appreciation of the importance of research and altruistic reasons. Participants' comments and reflections on their experience of participating in a fully online trial were positive and less than half of participants would have participated in the trial had it been conducted using other means of data collection. However participants identified trade-offs between the benefits and downsides of participating in Internet-based trials. The main trade-off was between flexibility and convenience - a perceived benefit - and a lack connectedness and understanding - a perceived disadvantage. The other tradeoffs were in the areas of: ease or difficulty in use of the Internet; security, privacy and confidentiality issues; perceived benefits and disadvantages for researchers; technical aspects of using the Internet; and the impact of Internet data collection on information quality. Overall, more advantages were noted by participants, consistent with their preference for this mode of research over others. The majority of participants (69%) would prefer to participate in Internet-based research compared to other modes of data collection in the future. Conclusion Participants in our survey would prefer to participate in Internet-based trials in the future compared to other ways of conducting trials. From the participants' perspective, participating in Internet-based trials involves trade-offs. The central trade-off is between flexibility and convenience - a perceived benefit - and lack of connectedness and understanding - a perceived disadvantage. Strategies to maintain the convenience of the Internet while increasing opportunities for participants to feel supported, well-informed and well-understood would seem likely to increase the acceptability of Internet-based trials.