Background Partnering with patients in healthcare research now benefits from a strong rationale and is encouraged by funding agencies and research institutions. However, this new approach raises ethical issues for patients, researchers, research professionals and administrators. The main objective of this review is to map the literature related to the ethical issues associated with patient partnership in healthcare research, as well as the recommendations to address them. Our global aim is to help researchers, patients, research institutions and research ethics boards (...) reflecting on and dealing with these issues. Methods We conducted a scoping review of the ethical issues and recommendations associated with partnering with patients in healthcare research. After our search strategy, 31 peer reviewed articles published between 2007 and 2017 remained and were analyzed. Results We have identified 58 first-order ethical issues and challenges associated with patient partnership in research, regrouped in 18 second-order ethical themes. Most of the issues are transversal to all phases and stages of the research process and a lot of them could also apply to patient-partnership in other spheres of health, such as governance, quality improvement, and education. We suggested that ethical issues and challenges of partnered research can be related to four ethical frameworks: 1) Research ethics; 2) Research integrity; 3) Organizational ethics, and 4) Relational ethics. Conclusions We have identified numerous ethical issues associated with the recent approach of patient-partnership in research. These issues are more diverse than the issues associated with a more traditional research approach. Indeed, the current discussion on how we address ethical issues in research is anchored in the assumption that patients, as research participants, must be protected from risk. However, doing research with, and not on, the patient involves changes in the way we reflect on the ethical issues associated with this approach to research. We propose to broaden the ethical discussion on partnered research to not only rely on a research ethics framework, but to also frame it within the areas of research integrity, organizational ethics and relational ethics. (shrink)