PURPOSE: West syndrome (WS) is a severe age-related acute epileptic encephalopathy of infancy characterized by infantile spasms, hypsarrhythmia and psychomotor delay. The aim of this study was to investigate if patients with WS had an altered autonomic output to the heart. METHODS: In 23 patients with WS the heart rate variability (HRV) was investigated by examining time- and frequency-domain parameters of HRV at the time of the diagnosis of hypsarrhythmia and compared to 22 age-matched controls. For the WS patients the same dataset was obtained and compared again at the end of the study period, when hypsarrhythmia was no longer present. RESULTS: Compared to controls, patients with WS during hypsarrhythmia had significantly lower SDNN (the standard deviation of the NN interval, i.e. the square root of variance) (19.2 ms; p = 0.007, Mann-Whitney\'s U-Test) and total power (242 ms(2); p = 0.044, Mann-Whitney\'s U-Test) in the awake state, indicating an abnormal autonomic output to the heart. Comparing the initial to the final examination demonstrated a significant increase in the HRV parameters SDNN (31.3 ms) and total power (757 ms(2); p = 0.001 and p = 0.013, Wilcoxon Signed Ranked Test). In addition, at the final examination the WS-patients no longer differed significantly from the controls. CONCLUSION: Our data suggest that the initial reduction in HRV in patients at the time of onset of WS is transient and related to the presence of hypsarrhythmia.