Background: Eliciting and considering patients preferences is essential to any clinical encounter and to good, high quality health care. Little research exists on how preferences are accommodated in decision making and how they influence treatment and rehabilitation. Aims: To explore perceptions of patients with musculoskeletal pain regarding how their preferences were accommodated in clinical decision making and influenced their rehabilitation, and whether their preferences changed during their rehabilitation. Methods: Qualitative interview study. Results: Participants preferences had, for the most part, influenced both choice of treatment and rehabilitation as a whole. While preferences were expressed to various extents, and largely perceived to be accommodated in the decision process, a good dialogue was considered essential for collaborative rehabilitation. Treatment decisions were to a large extent made jointly by the physiotherapist and the patient. Regardless of the strength of the preferences, participants appreciated the dialogue with the physiotherapist and the opportunity to discuss treatment options. The participants described how the physiotherapy episode of care had influenced their perceptions of and preferences for different treatment methods. Conclusions: The findings emphasise the importance of eliciting patient preferences, two-way communication and discussing treatment options, in order to stimulate collaborative rehabilitation.