BACKGROUND: There are no studies quantifying the nature of autonomic changes in absence epilepsy. Aims : We characterized the heart rate variability (HRV) during pre-interictal epileptiform discharges (IED), IED and post-IED states in absence epilepsy. MATERIAL AND METHODS: Electroencephalogram (EEG) records with generalized 3-Hz spike-wave discharges in 8 patients (M: F: 3 : 5; mean age: 13.0 +/- 2.5 years) with absence epilepsy were identified and corresponding electrocardiogram (ECG) time series were obtained. The time domain HRV measures were applied to pre-IED, IED and post-IED simultaneous ECG tracing. RESULTS: There was slight tachycardia during the IED phase (pre-IED: 90.15 +/- 3.45 bpm, IED: 94.82 +/- 4.63 bpm, P = 0.09) which returned to baseline during the post-IED phase (post-IED: 89.65 +/- 3.78 bpm). There was significant decrease in the standard deviation of RR interval (pre-IED: 40.0 +/- 4.15 ms, IED: 30.4 +/- 4.19 ms, P = 0.032) and trend in reduction of triangular index (pre-IED: 0.05 +/- 0.01, IED: 0.04 +/- 0.004, P = 0.08) during the IED phase when compared to pre-IED phase. The percentage of RR intervals >50 ms was lower during the IED phase and achieved significance when compared to post-IED phase (IED: 10.08 +/- 4.89, post-IED: 18.74 +/- 6.17, P = 0.050). While mean HR and RR interval significantly correlated with the duration of IEDs, there was no significant correlation between its duration with change in HRV parameters between the groups. There was no significant difference in HRV parameters between patients with long (>10s) and short (<10s) duration of IED. CONCLUSIONS: Transient increase in heart rate during IED phase was noted in patients with absence epilepsy. Longer duration of IED seems to be linked with significant tachycardia. While most HRV parameters did not reach statistical significance, standard deviation of RR intervals and triangular index was noted to be decreased during the IED phase and returns to pre-IED levels after the episode.