This paper identifies a number of significant gaps between the principles of good practice in research with children and the practical realities of conducting a research project with children. The context of the discussion is an ongoing research study of children and young people in Scotland with a parent or carer with HIV. The paper argues that conducting research with what is a hidden (and in many ways secret) population throws into sharp relief some difficulties and contradictions that are at the heart of the research process. The paper does not intend to present easy answers to the complex questions that it raises: the research project it describes is ongoing and not yet at the stage of disseminating findings in any definitive way. Moreover, it seems likely that there are no answers to the questions raised, but that the act of posing the questions may contribute to the development of better, more reflexive research with children.