BACKGROUND: Autonomic responses follow exposure to conditioned stimuli such as contextual factors associated with alcohol ingestion. Heart rate variability is under autonomic control and may be a measure of such response. METHODS: Twenty alcoholics and 23 matched social drinkers (all male) were exposed to a neutral cue and then an alcohol cue in identical settings, during which the electrocardiogram of these subjects was recorded. Time and frequency domain parameters of heart rate variability (HRV) were computed by a blind rater. RESULTS: Coefficient of variation of R-R intervals and absolute powers of HRV spectrum (in frequency bands 0.05-0.15 Hz and 0.01-0.05 Hz) following alcohol cue were significantly higher in alcoholics than social drinkers. The mean heart rate (MHR) failed to reflect this difference. CONCLUSIONS: HRV paradigm appears more sensitive than MHR to measure cue reactivity.