OBJECTIVE: The objective of this study was to determine whether interindividual variation in parasympathetic (cholinergic) and sympathetic (adrenergic) regulation of heart rate (as estimated by frequency components of heart rate variability [HRV]) may be accounted for, in part, by genetic variation in the choline transporter, a component of acetylcholine neurotransmission. METHODS: Resting HRV estimates of high- (HF) and low-frequency (LF) power and LF/HF ratio were determined from electrocardiogram recordings collected continuously over 5 minutes in 413 white individuals of European ancestry (49% men; aged 30-54 years [mean, 44 years]). Subjects were genotyped for a single nucleotide polymorphism (SNP) located in the 3\' untranslated region of the choline transporter gene (CHT1). Frequencies of the alternate CHT1 alleles, labeled G and T, were 76% and 24%. RESULTS: Compared with GG homozygotes, participants having any T allele had greater HF power (p <.02), lower LF power (p <.02), and lower LF/HF ratios (p <.005). Relative to men, women had lower LF power (p <.001) and lower LF/HF ratios (p <.005). CONCLUSIONS: These findings show that polymorphic variation in the CHT1 gene is associated significantly with interindividual variability in HRV indices related to parasympathetic (cholinergic) activity.