General practitioners are increasingly approached to participate in research and share de-identified patient information. Research using electronic health records has considerable potential for improving the quality and safety of patient care. Obtaining individual patient consent for the use of the information is usually not feasible. In this article we explore the ethical issues in using personal health information in research without patient consent including the threat to confidentially and the doctor-patient relationship, and we discuss how the risks can be minimised and managed drawing on our experience as general practitioners and researchers.