The social discovery of Gulf War-related illnesses, like other occupational and environmental disease, is firmly rooted in ongoing disputes over causation. Pressure from veterans groups, as well as intra-governmental disputes, have driven innovative research directions and challenged the dominant epidemiological paradigm. This dominant epidemiological paradigm was originally a position that viewed stress as the primary causal factor. In the emerging dominant epidemiological paradigm, researchers view veterans' symptoms as similar to other multi-symptom diseases and conditions, but with a firmer respect for the reality of those symptoms. In addition, some researchers pursue interactions between stress and physical exposure. We examine the evolution of the DEP to demonstrate that in many disease disputes, an affected population challenges government and science decision-making, and even ways of knowing, in an attempt to negotiate a disease definition and etiology that results in better treatment and prevention. After considerable research effort, only limited evidence has been found for environmental causation, and even many researchers sympathetic to veterans are doubtful that much more will be found. We analyze the social discovery and ongoing contestation of these illnesses, and the consequent effects on health and public policy. For extension to other disease disputes, we provide an overall model of disease discovery and contestation, examining the key forces of government, science, and citizens.