Much of Schaller's psychological research has examined the subtle cognitive processes that contribute to stereotypes and prejudices. One line of research focused on intuitive statistical reasoning processes. This work revealed that people form erroneous stereotypes when they engage in overly simplistic statistical reasoning, but that these erroneous stereotypes are less likely to emerge if people can be trained to engage in a more sophisticated reasoning process (analogous to a statistical analysis of covariance). Another line of research focused on communication processes as they relate to the emergence and change of group stereotypes. Additional lines of research, informed by the adaptationist reasoning characteristic of evolutionary psychology, focused on the ways in which specific kinds of perceived threats (e.g., threat of interpersonal violence), and contextual cues connoting vulnerability to those threats (e.g., ambient darkness), trigger specific kinds of prejudices against specific categories of people.

Within his program of research on threats and prejudices, Schaller developed a broader line of research on the perceived threat of infectious disease and its implications for psychological functioning. It this context, he coined the term "behavioral immune system" to refer to a suite of evolved psychological mechanisms that serve as a crude first line of defense against infectious diseases. The behavioral immune system includes sensory mechanisms that allow people to detect the presence of pathogens in objects (including people) in their immediate environment, as well as stimulus-response mechanisms that trigger aversive affective, cognitive, and behavioral reactions to those things (and persons). Schaller and his colleagues, as well as other behavioral scientists, have documented many implications that the behavioral immune system has for emotion, for prejudice, for human social cognition and social behavior more generally, for the origins of cross-cultural differences, and for actual immunological functioning.

Schaller has also published scientific research on a variety of other topics pertaining to human psychological functioning. These topics include: the implications of evolutionary fundamental human motives on social behavior, the psychology of kin recognition, and the psychological consequences of fame.