Elucidation of the cellular and molecular mechanisms of the circadian clock, along with the realization that these mechanisms are operative in both central and peripheral tissues, has revolutionized circadian biology. Further, these observations have resulted in an explosion of interest in the health implications of circadian organization and disorganization at both molecular and physiological levels. Thus, recent research has implicated mutations and polymorphisms of circadian clock genes in diabetes and obesity, cardiovascular disease, and cancer. At the neuro-behavioral level, circadian clock genes have also been implicated in sleep disorders, drug and alcohol addiction, and other psychiatric conditions. While such findings are frequently described as revealing "non-circadian" effects of clock genes, it remains possible that most of these non-circadian effects are in fact secondary to the loss of cellular and systemic rhythmicity. This review summarizes the evidence linking circadian clock genes to biobehavioral dysregulation, and considers criteria for defining a pleiotropic clock gene effect as non-circadian.