BACKGROUND: Noncompaction cardiomyopathy (NC) is a rare congenital heart disease characterized by progressive heart failure and life-threatening arrhythmias. Heart rate turbulence (HRT) has been defined as a noninvasive prognostic method to reveal the cardiac death risk in high-risk patients. OBJECTIVES: We aimed to assess the cardiac autonomic functions and their relations to the mortality in NC patients. METHODS: A total of 60 NC patients and 70 healthy controls were included in this study. All participants underwent 24-h Holter recording to assess the HRT parameters, included turbulence onset (TO), turbulence slope (TS), standard deviation of NN intervals of all normal beats (SDNN) and mean RR interval. RESULTS: NC patients had higher levels of TO than the control group (0.43 +/- 4.66% vs. -1.82 +/- 2.19%, p = 0.024), but the TS levels of NC patients were lower than those of the control group (3.43 +/- 3.28 vs. 4.94 +/- 2.86 ms/RR, p = 0.024). Thirteen patients died during follow-up (mean 83.3 +/- 32.5 months). TS was the strongest univariate mortality predictor (hazard ratio 10.01 [95% CI 2.22-42.52]; p = 0.004) in univariate Cox regression analysis. In multivariate analysis, LVEF </=0.40 and TS </=2.5 ms/RR interval were the only independent predictors of mortality (hazard ratio 5.29; p = 0.004, hazard ratio 13.45; p = 0.001, respectively). CONCLUSIONS: Patients with NC showed abnormal HRV and HRT parameters when compared to healthy subjects. Furthermore, impaired HRT reaction in NC is an independent predictor of mortality.