Adaptation is a continuous process between the genes of a particular species and its environment. Although a couple of weeks are long enough to adapt to some environmental changes, sometimes several generations are needed to adapt. Rapid and sustained environmental changes, however, exceed the adaptation capacity of species and cause gene-environment discordance. Genomes of individuals, who live at the beginning of such discordance, are adapted to the previous environment and therefore physiological mechanisms of the organism are inşuenced by this novel circumstance. The disrupted interaction between individual and environment appears as diseases, increased morbidity, and mortality in the phenotype. Diseases of civilizations which are the reşections of gene-environment discordance tend to accumulate into several main groups such as metabolic (e.g., cardiovascular, diabetes, hypertension, obesity and metabolic syndrome), reproductive (male and female infertility), neurodegenerative (e.g., Alzheimer, dementia) and some psychiatric disorders (e.g., major depression, bipolar disorders). In spite of the fact that the pathophysiology of many neuropsychiatric disorders are not well known, since symptoms including sleep and appetite problems, fatigue, loss of libido and concentration as well as metabolic disorders may coexist, it is considered that neuropsychiatric disorders may have a complex neurobiological basis. Some scientists have referred to this situation as a “neuropsychiatric syndrome” or “type II metabolic syndrome”. Data obtained from metabolic syndrome studies may be adapted to type II metabolic syndrome to clarify the biological basis of the disease. As seen in metabolic syndrome, the neuropsychiatric syndrome may also develop in a broken physiological infrastructure. Some of the disrupted physiological mechanisms shown in metabolic syndrome may be summarized as the mismanaged autonomic nervous system (ANS), reduced central and peripheral GABA production, and epigenetic perturbations which have recently become very popular. ANS dysregulation is closely related to recent treatment modalities such as vagal nevre stimulation (VNS) and light therapy (LT). Both modalities are based on the re-regulation of an already dysregulated autonomic rhythm. Secretion of melatonin from the pineal gland is one of the effective mechanisms in the regulation of ANS. Since melatonin is only used for the treatment of jet-lag and sleep problems, the range of treatment indications with melatonin has remained limited for years. Nevertheless, central effects of melatonin play an important role in the treatment of depression and similar disorders. Therefore, melatonin has been recently used to treat neuropsychiatric syndrome. Moreover, a severe familial tendency in neuropsychiatric disorders has long been recognised.