BACKGROUND Phototherapy is a common mode of treatment for neonatal hyperbilirubinemia. However, phototherapy has been reported to alter cardiovascular function by causing increased peripheral blood flow, diminished cardiac output and increased sympathetic activity that may be of concern particularly in sick or premature newborns. The effects of phototherapy on the autonomic nervous system modulation of heart rate in term neonates have not yet been investigated. OBJECTIVE The aim of the present study was to investigate the effects of phototherapy on the autonomic nervous system modulation of heart rate in healthy full-term jaundiced neonates. METHODS 30 full-term jaundiced infants were prospectively studied before and during phototherapy. Heart rate variability was analyzed with conventional time-domain, spectral, and time-dynamic techniques by using Poincaré plots. RESULTS Phototherapy was found to cause significant diminution in the short- and long-term variability of heart rate in newborns as documented by time-domain analysis of heart rate variability, and visually demonstrated by using Poincaré plots. Spectral indices and heart rate were unchanged during phototherapy. CONCLUSIONS A significant diminution in heart rate variability was documented during phototherapy, a phenomenon assumed to be centrally mediated. The reasons for this decrease are yet unknown. The use of time-dynamic analysis methods may offer important details on the newborn's physiology that cannot be revealed by traditional methods.