Serotonin (5-hydroxytryptamine; 5-HT) is a potent modulator of the physiology and behavior involved in generating appropriate responses to environmental cues such as danger or threat. Furthermore, genetic variation in 5-HT subsystem genes can impact upon several dimensions of emotional behavior including neuroticism and psychopathology, but especially anxiety traits. Recently, functional neuroimaging has provided a dramatic illustration of how a promoter polymorphism in the human 5-HT transporter (5-HTT) gene, which has been weakly related to these behaviors, is strongly related to the engagement of neural systems, namely the amygdala, subserving emotional processes. In this commentary, we discuss how functional neuroimaging can be used to characterize the effects of polymorphisms in 5-HT subsystem genes on the response of neural circuits underlying the generation and regulation of mood and temperament as well as susceptibility to affective illness. We argue that in time, such knowledge will allow us to not only transcend phenomenological diagnosis and represent mechanisms of disease, but also identify at-risk individuals and biological pathways for the development of new treatments.Keywords: Amygdala, emotion, FMRI, PET, prefrontal cortex, serotonin Converging evidence from animal and human studies using a myriad of experimental approaches has revealed that serotonin is a critical neurotransmitter in the generation and regulation of emotional behavior (Lucki 1998). Serotonergic neurotransmission has also been an efficacious target for the pharmacological treatment of mood disorders including depression, obsessivecompulsive disorder, anxiety and panic (Blier & de Montigny 1999). Moreover, genetic variation in several key 5-HT subsystems, presumably resulting in altered central serotonergic tone and neurotransmission, has been associated with various aspects of personality and temperament as well as susceptibility to affective illness (Murphy et al. 1998;Reif & Lesch 2003). Although many of these findings have led to novel insights about the neurobiology of complex behaviors and psychiatric disease, the enthusiasm for their collective results has been tempered by weak, inconsistent and failed attempts at replication.The inability to substantiate these relationships through consistent replication in independent cohorts may simply reflect methodological issues such as inadequate control for non-genetic factors (e.g., age, sex and population stratification), insufficient power and/or inconsistency in the methods applied. Alternatively, and perhaps more importantly, such inconsistency may reflect the underlying biological nature of the relationship between allelic variants in serotonin genes, each of presumably small effect, and observable behaviors in the domain of mood and emotion that typically reflect complex functional interactions and emergent phenomena. Simply put, genes do not encode behaviors. Biology dictates that allelic variants will most likely have a functional impact on the cellular and molecular pathw...