The role of theory in qualitative research is often underplayed but it is relevant to the quality of such research in three main ways. Theory influences research design, including decisions about what to research and the development of research questions. Theory underpins methodology and has implications for how data are analyzed and interpreted. Finally, theory about a particular health issue may be developed, contributing to what is already known about the topic that is the focus of the study. This paper will critically consider the role of theory in qualitative primary care research in relation to these three areas. Different approaches to qualitative research will be drawn upon in order to illustrate the ways in which theory might variably inform qualitative research, namely generic qualitative research, grounded theory and discourse analysis. The aim is to describe and discuss key issues and provide practical guidance so that researchers are more aware of the role theory has to play and the importance of being explicit about how theory affects design, analysis and the quality of qualitative research.