Serotonergic genes have been implicated in the pathogenesis of panic disorder and amygdala function in response to fearful stimuli. Regional brain activation on visual presentation of emotional facial stimuli was investigated in 20 patients with panic disorder by means of fMRI at 3 T. All patients were genotyped for the functional -1019C/G 5-HT1A and 5-HTTLPR polymorphisms. In patients homozygous for the 5-HT1A -1019G risk allele (n=5), fearful stimuli were associated with a decreased activation of right prefrontal cortex regions. Patients homozygous for the 5-HT1A -1019G risk allele or patients carrying the short risk allele of the 5-HTTLPR (n=13) showed higher amygdala activation in response to happy faces. This exploratory study suggests a role of the functional -1019C/G 5-HT1A and 5-HTTLPR polymorphisms on prefrontal cortex and amygdala activation patterns in response to emotional facial stimuli. These serotonergic polymorphisms might increase the risk for panic disorder by contributing to an altered processing of emotional stimuli.