At 33-34 weeks postconceptional age, the newborns from smoking mothers had lower HRV low frequency power normalised to the total spectral power (LF/TP) than the control group (median values: 8% vs. 15% respectively, p < 0.02). In the non-smoking group, RR-interval values and total HRV power were correlated with gestational age at birth, with a shorter RR and a lower total HRV power in lesser gestational ages (rho = 0.67, p = 0.03, rho = 0.71, p = 0.003 respectively). This correlation was not observed for RR values in the group with smoking mothers.