Research integrity is a well-established term used to talk and write about ethical issues in research. Part of its success might be its broad applicability. In this paper, we suggest that this might also be its Achilles heel, since it has the potential to conceal important value conflicts. We identify three broad domains upon which research integrity is applied in the literature: (1) the researcher (or research group), (2) research, and (3) research-related institutions and systems. Integrity in relation to researchers concerns character, although it remains to specify precisely what character traits are the desirable ones in this context and what values researchers should endorse. Integrity in relation to research concerns correct and sufficient description of the research process, data, results, and overall ‘research record’. Hence, it concerns the quality of research. However, whether or not this notion of research integrity covers all ethical aspects of research depends on whether one endorses a wider or a narrower interpretation of the ‘research process’. Integrity in relation to research-related institutions and systems leaves open whether they should be understood as agents in their own right or merely as means to research integrity. Besides the potential lack of clarity that our analysis reveals, we point to how this variety in uses might lead to concealment of value conflicts and propose an open discussion of central values.