Standardized heart rate analyses were performed in 60 drug-free patients with alcohol dependence, who were admitted consecutively to a psychiatric department, and in 60 healthy normal matched subjects. The procedure included time and frequency derived measurements of heart rate variability (HRV). The investigations were carried out 3 weeks after admission and treatment on a closed ward to avoid autonomic hyperexcitability during withdrawal or relapse. The patients showed a significantly increased heart rate (p < 0.05), a significant reduction in the coefficient of variation while resting (p < 0.01) and a significant decrease of the high frequency power of spectral analysis (p < 0.01) compared with the normal subjects. Cardiovascular autonomic dysfunction was found in 12 of the patients, but in only one of the normal subjects (p < 0.01). The results indicated moderate parasympathetic (vagal) alteration in alcohol-dependent patients treated in a psychiatric department. This may have implications for psychotherapeutic or psychopharmacological treatment strategies and prognosis in such patients with alcohol dependence.