1. Animal models of human behavior and disease are commonly used and have contributed significantly to progress in understanding the physiological mechanisms of both normal function and disease, and in the development of effective therapies. 2. Little attention has been given, however, to the scientific and ethical implications of choosing a particular animal model. 3. This paper discusses the rationale for the selection of particular animal models that have been chosen to study certain human diseases or behaviors, and provides examples to illustrate how underlying assumptions about methods and about physiological mechanisms and other relevant features of the disease or behavior of interest are embedded in the choice of an animal model. 4. Although these assumptions influence the direction of research, they are rarely analyzed explicitly, or evaluated empirically. The authors recommend that assumptions should be clearly stated and that, whenever possible, they be specifically and thoroughly evaluated empirically.