Blushing is considered to be one of the prime pathophysiological markers of social anxiety disorder, potentially mediated by serotonergic function. Therefore, in the present study 62 patients with social anxiety disorder and 62 age- and sex-matched healthy controls were investigated for the influence of serotonin transporter (5-HTT) gene variation (5-HTTLPR, rs25531) on blushing propensity as measured by the blushing propensity scale (BPS). The less active 5-HTTLPR genotypes were nominally significantly associated with increased blushing propensity in patients with social anxiety disorder as compared to controls with an equidirectional trend for the less active 5-HTTLPR/rs25531 haplotypes. Even when statistically controlled for influence of depression, this association remained significant. In summary, the present pilot study suggests a potential role of functional serotonin transporter gene variation in blushing propensity warranting replication and encouraging genetic analyses of further intermediate phenotypes of social anxiety disorder.