General practice uses an eclectic range of research methodology. This includes increasing reliance upon qualitative research methods. There seem to be two distinct treatments of qualitative research within primary care and, in particular, within general practice research. The first is characterized by a purely utilitarian and technical focus, using a qualitative method because it is the most appropriate means of realizing the aims of the research, while the second is characterized by in-depth engagement with the philosophical and paradigmatic aspects of qualitative methodology. In-depth engagement with methodology and theory, and theory building, is an important aspect of masterate and doctoral research within social sciences such as education and anthropology, and in the discipline of nursing, but has not been a feature of qualitative research in medicine. A practical difficulty encountered within postgraduate programmes such as the one in which the author teaches is that when innovative qualitative techniques are used by GPs in their postgraduate research dissertations and theses, it is often beyond GP examiners' own knowledge and experience, yet it fails to measure up to standards established in social sciences, particularly in sociology and anthropology where in-depth reflexive engagement with the theory and philosophy of qualitative methodology is expected. This paper suggests that the value of in-depth engagement with methodology when conducting qualitative research results in creative and innovative ways of conducting research that are consonant with the nature of general practice itself, and strengthens research findings. Therefore, as teachers of research methods and supervisors of research theses, it is important to encourage students conducting qualitative research to engage fully with theoretical and methodological issues.