While affective and anxiety disorders are substantially heritable, their inheritances are complex and multifactorial. 1 It is therefore unsurprising that such etiologically heterogeneous illnesses have not easily succumbed to genetic methodologies that are further challenged by an imperfect classification system. 2 Nevertheless, investigators continue to behave as if the problems are not insoluble. Association studies of candidate genes have lately held particular appeal, at least partly since this approach connects well with the familiar view that these disorders arise from alterations in particular brain neurochemical systems.The evidence implicating brain serotonin (5-HT) neurotransmission in anxiety and affective disorders is extensive and compelling. 3,4 In the attempt to investigate whether alterations in function of brain 5-HT systems are etiologically associated with these illnesses, attention has focused on polymorphisms in genes encoding components of the serotonergic system. These genes are seen as potential candidates influencing susceptibility, course, or symptoms. Researchers are investigating variants of genes for the 5-HT synthesis pathway, the 5-HT transporter (5-HTT), and several of the numerous 5-HT receptors. Potentially important sequence variations may occur in the coding region of a gene, in gene promoters (which could affect transcription efficiency), and in intronic regions, which, while non-coding, might affect gene expression or distribution of the gene product. Some variants of serotonin system genes are common, consistent with a role in complex, polygenic disorders with relatively high population incidences.The most common research strategy used in association studies, because it is often logistically easiest, is the population-based approach. Such studies compare the frequencies of polymorphic alleles in a group of individuals with a particular psychiatric diagnosis with those in a reference population. The use of this method is now widespread. Although this strategy has important limitations (see below), initial findings have been intriguing enough to spur further research by diverse groups of investigators.A number of reports have described associations between affective disorders and polymorphisms in or near the 5-HTT gene. The 5-HTT is a major modulator