The functional Catechol-O-methyltransferase (COMT Val 108/158 Met) polymorphism has been shown to have an impact on tasks of executive function, memory and attention and recently, tasks with an affective component. As estrogen may downregulate COMT, we were interested in the effect of gender, COMT genotype and the interaction between these factors on brain activations during an affective processing task. We used functional MRI to record brain activations from 74 healthy subjects who engaged in a facial affect recognition task; subjects viewed and identified fearful faces compared to neutral faces. We found a significant effect of gender on brain activations in the left amygdala and right superior temporal gyrus, where females demonstrated increased activations over males. Within these regions, female val/val carriers showed greater activity compared to met/met carriers, while male participants with a met/met allele showed greater deactivations compared to val/val carriers. There was no main effect of the COMT polymorphism, gender or genotype by gender interaction on task performance. We propose that the observed effects of gender and COMT allele on brain activations arise from differences in dopamine levels in these groups and that the gender differences and gender genotype interaction may be due to the downregulation of COMT by estrogen.