New diseases in humans and animals have been the subject of considerable research as well as policy development and popular attention. Researchers commonly proceed on the basis of plausible assumptions about mechanisms, pathways, and dangers but seldom question the assumptions themselves. Studies in the history and sociology of science show that research trajectories are conditioned by social, political, and economic arrangements. The assumptions underlying research into three new diseases-devil facial tumor disease in Tasmanian devils, AIDS in humans, and leukemia in soft-shell clams-are examined, and dominant and alternative research programs compared. In each case, most research has assumed the disease is spread through "natural processes", while research about possible human influences has been left undone.