Concerns about the welfare of agricultural animals in corporate or “factory farming” systems are growing. Increasingly, it is suggested that modem farm animal production practices are morally objectionable, causing physical and mental suffering to animals. Such criticisms are premised on beliefs about the mental capacities of farm animals that are not wholly supported by scientific evidence, for little is known about farm animal cognition. Some animal scientists, realizing that concerns about the treatment of agricultural animals cannot be addressed in absence of knowledge about farm animal mentality, have begun cognitive studies of farm animals. Subsequently, several ethical problems have emerged. In this paper it is argued that while farm animal cognition studies are needed, scientists must consider the moral problems and implications of the research, and must devise empirically testable hypotheses about those aspects of cognitive behavior that are relevant to discussions about moral treatment of farm animals.