Research Ethics Committees (RECs) are frequently a focus of complaints from researchers, but evidence about the operation and decisions of RECs tends to be anecdotal. We conducted a systematic study to identify and compare the ethical issues raised in 54 letters to researchers about the same 18 applications submitted to three RECs over one year. The most common type of ethical trouble identified in REC letters related to informed consent, followed by scientific design and conduct, care and protection of research participants, confidentiality, recruitment and documentation. Community considerations were least frequently raised. There was evidence of variability in the ethical troubles identified and the remedies recommended. This analysis suggests that some principles may be more institutionalized than others, and offers some evidence of inconsistency between RECs. Inconsistency is often treated as evidence of incompetence and caprice, but a more sophisticated understanding of the role of RECs and their functioning is required.