The aim of the present study was to examine cardiac autonomic function during acute alcohol withdrawal (AW) in two clinical subgroups with alcohol dependence. To this end we compared 24 patients with pure alcohol dependence (Pure ALC) with 24 alcohol-dependent patients who had comorbid symptoms of anxiety and/or depression (ANX/DEP ALC) on their mean heart rate and several (spectral) measures of heart rate variability (HRV) obtained from the patients when they were withdrawn from alcohol. To elucidate the contribution of anxiety and depression to the cardiac measures we moreover compared these groups to 120 non-comorbid patients with major depressive disorder (MDD), 24 patients with anxiety disorders and 120 matched controls. The Hamilton Depression Rating Scale (HAM-D) and the Hamilton Anxiety Rating Scale (HAM-A) were employed for the clinical symptom ratings. The cardiac measures were found to significantly discriminate among the groups (Hotelling-Lawley F = 3.18, p < .001). Post hoc testing revealed that total HRV (variance in interbeat intervals) was reduced in Pure ALC (p = .033, Cohen’s d = −0.51), ANX/DEP ALC (p < .001, Cohen’s d = −1.33), MDD (p < .001, Cohen’s d = −0.66), and anxiety disorders (p = .002, Cohen’s d = −0.69), relative to controls. When these comparisons were adjusted for smoking history in pack-years, the results were unchanged. The ANX/DEP ALC patients showed significantly greater reduction in total HRV and high frequency (HF)-HRV compared with the Pure ALC patients. Both anxiety and depression moderated the influence of alcohol use and withdrawal on resting HRV. Our results suggest that compared to Pure ALC, ANX/DEP ALC presents a subtype of alcohol dependence with higher vulnerability to reduced HRV during acute AW. Implications for cardiovascular risk are discussed.