CONTEXT: Autonomic nervous system imbalance is related to cardiovascular risk. Heart rate variability (HRV) indexes are associated with age, race, and sex, but the role of sex hormones is still unknown. OBJECTIVE: To evaluate sympathovagal balance (SB) in transsexuals. PATIENTS: Eighteen transsexual subjects, 12 male-to-female (group 1) and 6 female- to-male (group 2), compared with 34 age-matched controls: 17 males (group 3) and 17 females (group 4). Autonomic testing of SB was performed by Power Spectral Analysis (PSA) of HRV in clinostatism (c) and orthostatism (o). PSA identifies power peaks: high frequency (HF) expresses vagal activity, while low frequency (LF) expresses sympathetic activity. RESULTS: Group 1 showed lower LFc than groups 2, 3, and 4 (p<0.001, p=0.05, p<0.001, respectively), and lower LFo than groups 3 and 4 (p=0.01); HFc was lower than in groups 2, 3, and 4 (p=0.02, p=0.02, p<0.001, respectively), and HFo was lower than in groups 3 and 4 (p<0.001). LFo/HFo ratio was higher in group 1 than in group 4 (p<0.001). No differences emerged between groups 2 and 3. Group 2 showed lower HFo than group 4 (p=0.03), and a higher LFo/HFo ratio (p=0.01). Group 3 showed lower HFo and HFc than group 4 (p=0.02, p=0.05, respectively), and a higher LFo/HFo ratio (p=0.03). CONCLUSION: In this study we found a sympathovagal imbalance due to a reduced sympathetic and parasympathetic influence on heart rate. Sex hormone therapy per se may play a role in this imbalance, and HRV measurement could be useful in detecting cardiovascular risk in transsexuals.