The heart rate variability, modulated by autonomic nervous system, has been reported to decrease in depression of the central nervous system, especially of the brainstem. To assess the brainstem dysfunction, we analyzed R-R interval values (the intervals between R waves of ECG) in 9 children (7 in comatose children and 2 in central apnea) by spectral analysis using an autoregressive model. The findings of spectral analysis were compared with those of auditory brainstem response (ABR). In comatose children with the brainstem dysfunction, the reduction of the total power was apparent before the appearance of ABR abnormality. In central apnea due to the dysfunction of respiratory center in brainstem, only the respiratory component decreased without the reduction of the total power or ABR abnormality. Spectral analysis of the heart rate variability is a useful means for assessment of the brainstem function.