Background Research is fundamental to improving the quality of health care. The need for regulation of research is clear. However, the bureaucratic complexity of research governance has raised concerns that the regulatory mechanisms intended to protect participants now threaten to undermine or stifle the research enterprise, especially as this relates to sensitive topics and hard to reach groups. Discussion Much criticism of research governance has focused on long delays in obtaining ethical approvals, restrictions imposed on study conduct, and the inappropriateness (...) of evaluating qualitative studies within the methodological and risk assessment frameworks applied to biomedical and clinical research. Less attention has been given to the different epistemologies underlying biomedical and qualitative investigation. The bioethical framework underpinning current regulatory structures is fundamentally at odds with the practice of emergent, negotiated micro-ethics required in qualitative research. The complex and shifting nature of real world settings delivers unanticipated ethical issues and (occasionally) genuine dilemmas which go beyond easy or formulaic ‘procedural’ resolution. This is not to say that qualitative studies are ‘unethical’ but that their ethical nature can only be safeguarded through the practice of ‘micro-ethics’ based on the judgement and integrity of researchers in the field. Summary This paper considers the implications of contrasting ethical paradigms for the conduct of qualitative research and the value of ‘empirical ethics’ as a means of liberating qualitative (and other) research from an outmoded and unduly restrictive research governance framework based on abstract prinicipalism, divorced from real world contexts and values. (shrink)