Recent studies have investigated the association between serotonin transporter gene promoter (5-HTTLPR) functional polymorphisms and attentional biases to threat, a cognitive mechanism that probably contributes to the development and maintenance of anxiety. The present study genotyped a sample of N = 141 healthy volunteers for an insertion/deletion polymorphism and the rs25531 single-nucleotide polymorphism in 5-HTTLPR. In order to investigate attentional biases to threat, we used a probe discrimination task in which the gaze direction of centrally presented fearful or neutral faces endogenously cued attention. The results indicated no significant differences in attentional biases to threat between 5-HTTLPR genotype groups. However, we found that carriers of two low-expressing alleles (i.e., S or LG) of 5-HTTLPR displayed a significant slowing of responses across trials with fearful compared to neutral faces. This effect may indicate that fearful faces triggered increased emotional arousal in these genotypes, which may have interfered with the processing of gaze direction and spatial cuing. These results suggest that using fearful faces as endogenous spatial cues may be problematic in genotypes associated with facilitated emotional arousal to these stimuli, and underscore the hypothesis that 5-HTTLPR specifically influences automatic rather than consciously-controlled processes of attention.