BACKGROUND: The congenital long QT syndrome (LQTS) affecting myocardial repolarization is caused by mutations in different cardiac potassium or sodium channel genes. Adrenergic triggers are known to initiate life-threatening torsade de pointes ventricular tachycardias in LQTS patients, and anti-adrenergic therapy has been shown to be effective in many cases. Despite this well-documented adrenergic component, the data about autonomic modulation of the heart rate in LQTS, as described by heart rate variability (HRV) analysis, are very limited. METHODS: Conventional time- and frequency-domain and newer nonlinear measures of HRV were compared in resting conditions among 27 LQTS patients with gene mutations at the LQT1 (n = 8), LQT2 (n = 10) or LQT3 (n = 9) loci and 34 LQTS noncarrier family members. RESULTS: None of the conventional time- or frequency-domain or newer nonlinear measures of HRV differed significantly between the LQTS carriers and LQTS noncarriers or between the LQT1, LQT2, and LQT3 carriers. CONCLUSIONS: These findings suggest that baseline cardiac autonomic modulation of the heart rate measured in resting conditions by traditional or newer nonlinear measures of HRV is not altered in LQTS patients. Furthermore, no differences are observed in HRV parameters between LQTS patients with potassium (KvLQT1, HERG), and sodium (SCN5A) ion channel gene mutations. HRV analysis in resting conditions does not improve phenotypic characterization of LQTS patients.