The ethics of conducting research in epidemic situations have yet to account fully for differences in the proportion and acuteness of epidemics, among other factors. While epidemics most often arise from infectious diseases, not all infectious diseases are of epidemic proportions, and not all epidemics occur acutely. These and other variations constrain the generalization of ethical decision-making and impose ethical demands on the individual researcher in a way not previously highlighted. This paper discusses a number of such constraints and impositions. It applies the ethical principles enunciated by Emmanuel et al.(1) to the controversial Pfizer study in Nigeria in order to highlight the particular ethical concerns of acute epidemic research, and suggest ways of meeting such challenges. The paper recommends that research during epidemics should be partly evaluated on its own merits in order to determine its ethical appropriateness to the specific situation. Snap decisions to conduct research during acute epidemics should be resisted. Community engagement, public notification and good information management are needed to promote the ethics of conducting research during acute epidemics. Individual consent is most at risk of being compromised, and every effort should be made to ensure that it is maintained and valid. Use of data safety management boards should be routine. Acute epidemics also present opportunities to enhance the social value of research and maximize its benefits to communities. Ethical research is possible in acute epidemics, if the potential challenges are thought of ahead of time and appropriate precautions taken.