OBJECTIVE: Assess the autonomic function in hypertrophic cardiomyopathy (HCM) through heart rate variability (HRV) and to correlate it to echocardiographic data. METHODS: Two groups were studied, and compared for gender, age and HR: A) Ten (10) patients reporting septal HCM (70% non-obstructive); B) Ten (10) healthy volunteers. HRV was analyzed along four successive stages: at rest, under controlled breathing, while bending, and controlled breathing associated to bending. Variables means were compared between groups and intra-groups in the different stages; in Group A, variables means were correlated to echocardiographic measurements (interventricular septum and left atrial diameter). RESULTS: No HRV difference was reported among groups in the first 3 stages. In the fourth stage vagal activity was shown to be higher in Group A [quadratic mean log between RR intervals (RMSSD) - 1.35+/-0.14 vs 1.17+/-0.16; p=0.019; high frequency component logarithm (LogHF)- 4.89+/-0.22 vs 4.62+/-0.26; p=0.032]. Along the stages, vagal measurements [rate of pairs of consecutive RR intervals whose difference is > or =50 ms (pNN50) and LogHF] also showed lower reduction in the third stage in Group A, while LogHF showed some increase in last stage (p=0.027), thus indicating marked parasympathetic activity in that group. Group A HRV analysis showed no difference among patients reporting larger hypertrophy or atrial diameter. CONCLUSION: 1) Parasympathetic prevalence was shown during autonomic stimulation in HCM patients; 2) No correlation was found between HRV and echocardiographic measurements under analysis.