BACKGROUND: Nonreassuring fetal status (NRFS) refers to a compromised fetal condition which implies hypoxia. The influence of intrapartum hypoxia on autonomic nervous system function in early postnatal life is unknown. This study explored the influence of NRFS on the heart rate variability (HRV) of newborn infants. METHODS: Singleton newborn infants delivered through Cesarean delivery (CD) with indications of elective purpose (n = 32), dystocia (n = 29), or NRFS (n = 22), and through vaginal birth (VB) (n = 80) were consecutively collected. HRV parameters including standard deviation of average NN intervals (SDANN), low frequency (LF), high frequency (HF), LF%, HF%, and total power (TP), were obtained for analysis in 3 days postpartum. An independent t-test or one-way ANOVA was used to compare differences in numeric data. RESULTS: SDANN, HF, HF%, and TP of newborn infants in the VB group were significantly higher than those in the CD group. The NRFS group had significantly lower SDANN, HF, and TP than those of the elective group, and significantly lower HF, HF%, and TP than those of the dystocia group. CONCLUSIONS: Newborn infants delivered through Cesarean section had lower HRV, especially those who experienced NRFS during labor. The long-term effects of changes of HRV in neonates require further evaluation.