Facilitating patient choice is an important element in respecting the autonomy of patients. Evidence-based medicine has the potential to contribute to this process by the provision of high quality research-based information, for use by patients and clinicians. In this paper, I analyse the processes of evidence-based medicine in order to identify the ways in which patient choice is affected by decisions made in the development and use of evidence-based guidelines. I argue that despite the potential contribution, the current methods and techniques of guideline production limit rather than facilitate patient choice.