Individual differences in brain response to emotional stimuli have previously been associated with gene variations within the serotonin transporter (5-HTT) and tryptophan hydroxylase-2 (TPH2) genes. We recently reported that these two genes exhibit an additive effect, based on recordings of event-related potentials (ERPs) from individuals viewing emotional scenes. The current study was designed to replicate and extent this initial report in an independent study sample, and use functional magnetic resonance imaging (fMRI) to identify specific neural loci that may mediate the 5-HTT–TPH2 additive effect. Furthermore, we sought to obtain convergent evidence for a gene–gene additive effect by collecting fMRI data from the same individuals engaged in two different cognitive-affective tasks, using emotional and neutral facial expressions and word stimuli. We found evidence for an additive effect of 5-HTT–TPH2 genotype, which was most robust in the putamen, a region rich in both 5-HTT and TPH2 protein, but was also observed in the amygdala at a less stringent threshold, and in other cortical regions. The additive effect was more robust effect for visuospatial than for verbal stimuli, and more robust for negatively than for positively valenced stimuli. These findings confirm and extend the additive effect of two critical genes in the serotonergic regulation of neural processing of affective stimuli, and identify the striatum as a critical site where is gene–gene regulation takes place.