The relationship between heart rate variability and respiration patterns was investigated using spectral analysis techniques in nine full-term infants whose ages ranged from 39-75 h. All the infants were studied during sleep, although no attempt was made to classify rapid eye movement or nonrapid eye movement states prospectively. The data obtained were examined to determine which aspects of neonatal breathing patterns are correlated with heart rate variability. Three spectral regions of heart rate variability could be identified: a very low frequency region below 0.02 Hz; a low frequency region from 0.02-0.20 Hz; and a high frequency region above 0.20 Hz. The dominant heart rate variability activity in these neonates was seen in the very low and low frequency regions, with little activity in the high frequency regions. In contrast to older infants and adults, respiration and heart rate variability were not strongly related through a high frequency region respiratory sinus arrhythmia but rather through a breath amplitude sinus arrhythmia which occurs in the low frequency region of the spectrum. The prominent very low frequency activity and the low frequency activity ascribed to breath amplitude modulation may result from autonomic nervous system mediation of chemoregulation.