Objectives: To explore general practitioners' perceptions of their preparedness for an influenza pandemic, the changes they would make to their practice, and the ethical justifications for their planned actions. Design and setting: A qualitative study was performed among South Australian GPs between March and October 2007. A semi-structured interview was carried out with each participant in his or her practice, and the interviews were audio-recorded, transcribed and analysed thematically. Participants: 10 GPs were recruited: five from a metropolitan Division and five from a rural Division of General Practice. Results: Some participants felt they would not be able to cope with an influenza pandemic, while others felt it would simply mean an increase in their workloads. Most respondents considered creating separate waiting rooms, moving the reception desk outside of the practice and delaying all non-urgent consultations in order to deal with a pandemic more effectively. Respondents mentioned the conflict between their various roles and responsibilities as a primary source of tension when thinking about the way they would organise their work in the event of a pandemic. A number of GPs said they would not practise in the event of a pandemic, as they felt their responsibility to their families outweighed that to their patients. Conclusions: Professional codes of ethics should include guidance about the scope of the duty to treat during infectious disease outbreaks. The community has to uphold the value of reciprocity, and ensure that GPs and their families are provided with support during a pandemic and are given the opportunity to be actively involved in pandemic preparedness planning.