Panic disorder is an anxiety disorder with an estimated heritability of up to 48%. The functional val158met polymorphism in the catechol-O-methyltransferase (COMT) gene has been found to be associated with panic disorder and to influence limbic and prefrontal brain activation in response to unpleasant stimuli. In the present study, neuronal activation following emotional stimulation was used as an endophenotype and investigated for association with the COMT val158met polymorphism in panic disorder. Twenty patients with panic disorder were scanned by means of functional magnetic resonance imaging at 3 Tesla under visual presentation of emotional faces and genotyped for the COMT val158met polymorphism. In response to fearful faces, increased activation in the right amygdala was observed in patients carrying at least one 158val allele. Increased activation or less deactivation associated with the 158val allele was seen upon presentation of fearful, angry and happy faces in the orbitofrontal and ventromedial prefrontal cortex, respectively. Our data provide preliminary evidence for a role of the functional val158met COMT polymorphism in amygdala and prefrontal activation in response to emotional faces in panic disorder. This COMT variant might increase the vulnerability to panic disorder by modulating dopaminergic tonus in relevant brain regions and thus altering neuronal processing of anxiety-related emotional cues.