Abstract The use of qualitative research in empirical bioethics is becoming increasingly popular, but its implementation comes with several challenges, such as difficulties in aligning moral epistemology and methods. In this paper, we describe some problems that empirical bioethics researchers may face; these problems are related to a tension between the different poles on the spectrum of scientific paradigms, namely a positivist and interpretive stance. We explore the ideas of narrative construction, ‘genres’ in medicine and dominant discourses in relation to empirical research. We also reflect on the loss of depth and context that may occur with thematic or content analyses of interviews, and discuss the need for transparency about method...