Case-control association studies use genetic markers as putative etiologic risk factors. The approach is controversial and has tended to produce associations in neuropsychiatry that do not stand the test of time. We studied the processes that can bias the outcomes away from a true representation of the relationship between a genetic marker and a neuropsychiatric disorder. If conducted with care and mindfulness of the potential pitfalls, case-control association studies can be an important tool for psychiatric genetic research.