BACKGROUND: Primary health care clinicians are being encouraged to undertake qualitative research, however the in-depth interviewing skills required are not as straightforward as might be first supposed. While there are benefits and certain skills that clinicians can bring to interview-based research, there are important new skills to develop. To date there has been neither discussion about these new skills, nor any preparatory guidelines for clinicians entering into interview-based research in the qualitative research literature. In the absence of formal guidelines, we suggest the use of reflexivity throughout the interview process as a means to become more accomplished in this area. We present our own experiences as a novice general practitioner (GP) researcher undertaking a PhD study and her experienced supervisors. The PhD study used critical phenomenology through in-depth interviews to understand the experience of the patient-doctor relationship between same-sex attracted women and their usual GP in Australia. RESULTS: We used reflexivity to improve the rigour of the data collection. This enabled improved probing, fewer assumptions, avoidance of premature interpretation, and an accentuated sense of curiosity during interviews. We also enlisted reciprocity between interviewer and interviewee as a tool to improve engagement and trust, share interview control, and ultimately improve the depth of the interview content. CONCLUSION: Preparatory recommendations for novice clinician research interviewers include the importance of recognising the multiple identities that they bring to the interview. In this setting in particular this involves acknowledging the clinician interviewer as a potential insider in relation to interviewees and negotiating shared understanding to avoid insider assumptions. Other essential requirements are having an experienced research supervisor, arranging pilot interviews that include active feedback on interviewing style from interviewees, and being reflexive during interviews. More formal guidelines for in-depth interviewing skills development are needed.