Background: Clinical practice guidelines are largely conceived as tools that will inform health professionals' decisions rather than foster patient involvement in decision making. The time now seems right to adapt clinical practice guidelines in such a way that both the professional's perspective as care provider and the patients' preferences and characteristics are being weighed equally in the decision-making process. We hypothesise that clinical practice guidelines can be adapted to facilitate the integration of individual patients' preferences in clinical decision making. This research protocol asks two questions: How should clinical practice guidelines be adapted to elicit patient preferences and to support shared decision making? What type of clinical decisions are perceived as most requiring consideration of individual patients' preferences rather than promoting a single best choice? Methods: Stakeholders' opinions and ideas will be explored through an 18-month qualitative study. Data will be collected from in-depth individual interviews. A purposive sample of 20 to 25 key-informants will be selected among three groups of stakeholders: health professionals using guidelines (e. g., physicians, nurses); experts at the macro-and meso-level, including guideline and decision aids developers, policy makers, and researchers; and patient representatives. Ideas and recommendations expressed by stakeholders will be prioritized by nominal group technique in expert meetings. Discussion: One-for-all guidelines do not account for differences in patients' characteristics and for their preferences for medical interventions and health outcomes, suggesting a need for flexible guidelines that facilitate patient involvement in clinical decision making. The question is how this can be achieved. This study is not about patient participation in guideline development, a closely related and important issue that does not however substitute for, or guarantee individual patient involvement in clinical decisions. The study results will provide the needed background for recommendations about potential effective and feasible strategies to ensure greater responsiveness of clinical practice guidelines to individual patient's preferences in clinical decision-making.