The ethics of medical research have grown as an area of expertise and debate in recent years, with two broad approaches emerging in relation to transnational research: (1) the refinement of guidelines and strengthening of review, processes primarily to protect the right of individual research participants and strengthen interpersonal relations at the micro-level; and (2) considering more centrally, as crucial ethical concerns, the wider interests of whole populations, the functioning of research institutions, the processes of collaboration, and the ethics of inequitable international relations. We see the two areas of debate and action as complementary, and believe that social science conducted in and around transnational medical research environments can bring these two perspectives together in a more 'situated ethics' of research. To explore this idea for medical research in Africa, we organized a conference in December 2005 in Kilifi, Kenya. In this introduction we outline the two emerging approaches to medical ethics, summarise each of seven papers selected from the conference for inclusion in this special issue on ethics and ethnography, and finally highlight two areas of lively debate at the conference itself: the appropriateness and value of ethics guidelines and review boards for medical research; and the ethical review of social science research. Together, the papers and debates point to the importance of focusing on the ethics of relationships and on justice in both biomedicine and social science research, and on giving greater voice and visibility to the field staff who often play a crucial and under-supported role in 'doing ethics' in the field. They also point to the potential value of social science research on the range of relationships operating at different levels and time scales in medical research, including those surrounding community engagement activities, and the role and functioning of ethics review boards. We conclude by highlighting the ethical priority of capacity strengthening in medical research, social science and research ethics in Africa to ensure that local and national priorities and concerns are considered at both the micro and macro levels.