In clinical psychopharmacology, the existence of marked inter-individual differences in both outcome and side effects is a common observation. Consequently, pharmacogenetics has also gained an increasing interest in psychiatry. Recent exciting findings seem to suggest that the growing interest in regulatory regions of candidate genes and neurotransmitters metabolism, together with the application of sophisticated molecular approaches, may offer new opportunities in neuropsychopharmacology. Indeed, quantitative variation of gene expression and/or of neurotransmitters metabolism could better explain both psychopathology and clinical response to psychotropic drugs. Three functional polymorphisms, and their possible relationship with clinical variables, are discussed. The first is the 44-bp insertion/deletion reported in the promoter region of the serotonin transporter gene. A functional repeat polymorphism in the promoter region of the gene encoding for the enzyme monoamine oxidase A represents the second example. The last is a functional polymorphism within the coding region of the gene encoding for the enzyme catechol-O-methyltransferase