A common polymorphism of the brain-derived neurotrophic factor (BDNF) gene (Val66Met) has been implicated in anxiety, which is associated with lower vagal activity. We hypothesize that the BDNF Val66Met polymorphism may have a modulatory effect on the cardiac sympathovagal balance. A total of 211 healthy Chinese-Han adults (58 male, 153 female, aged 33.3 +/- 10.3 years) were recruited with three BDNF genotypes: Val/Val (47, 22.3%), Val/Met (108, 51.2%), and Met/Met (56, 26.5%). Autonomic function was assessed via an analysis of heart rate variability. Reductions in high-frequency power, an index for parasympathetic activity, and increases in the low-frequency/high-frequency ratio, an index for sympathovagal balance, were found in subjects bearing the Met/Met genotype as compared to the Val/Val group. These results suggest that an altered sympathovagal balance with relatively decreased parasympathetic activity is associated with the Met/Met genotype, suggesting a potential role for the studied BDNF polymorphism in modulating cardiac autonomic functions.