BACKGROUND: Isolated left venticular noncompaction (IVNC) is a rare congenital heart disease charactrized by a pattern of an excessively prominent trabecular meshwork with deep intertrabecular recesses. Heart rate variability (HRV) has been reported to be impaired in various heart diseases, though little is known regarding HRV in adult patients with IVNC. METHODS: We measured spectral components of HRV using fast Fourier transformation of 24-h Holter recordings in 10 adult patients with IVNC, 40 patients with myocardial infarction (MI), 40 patients with hypertrophic cardiomyopathy (HCM) and 40 healthy controls. RESULTS: The low frequency component and the high frequency component of HRV were lower in IVNC patients tahn those in controls (265 +/- 213 ms(2) vs. 469 +/- 195 ms(2), p < 0.01; 80 +/- 51 ms(2) vs. 185 +/- 126 ms(2), p < 0.01). Furthermore, 3 IVNC patients with a previous history of heart failure exhibited more decreased HRV (low frequency, 75 +/- 56 ms(2); high frequency, 39 +/- 18 ms(2)). Contrary, the ratio of low frequency to high frequency component was higher in patients with IVNC than controls (3.5+/-0.5 vs. 3.2 +/- 0.3, p < 0.05). The degree of impaired HRV was severest in MI patients, intermediate in IVNC patients and mildest in HCM patients compared with controls. CONCLUSIONS: HRV is impaired in adult patients with IVCN, especially in patients with a previous history of heart failure, suggesting vagal withdrawal or sympathetic enhancement. HRV in IVNC adults is less impaired than in MI patients, and more impaired than in HCM patients of our cohort.