Abstract Background Disturbances in maternal physiology can cause changes in the fetal condition that may lead to impaired fetal development. Synchronous monitoring of cardiac autonomic tone via the assessment of the fetal and maternal heart rate (HR) and heart rate variability (HRV) may provide an appropriate diagnostic window. Methods Partial rank correlation coefficients between the maternal and fetal HR and HRV indices were calculated and verified by testing surrogate data in 315 magnetocardiographic (MCG) recordings from 141 healthy women pregnant with singleton fetuses [18+6 to 39+2 weeks gestational age (WGA)]. We assessed maternal self-perceived depression, anxiety and stress by means of the Depression, Anxiety, Stress Scales self-reporting instrument (DASS42G) questionnaire. Results The maternal HRV correlated positively with the fetal HRV, but negatively with the fetal HR. Correlation was |r|<0.2 in state-independent and gestational age (GA) <32 weeks, but |r|>0.2 in active sleep and GA ≥32 weeks. The DASS42G results correlated with the maternal HRV and HR, while the fetal HR and HRV were not influenced. Conclusion Correlations between maternal and fetal autonomic activation were statistically confirmed. They depend on the GA and active fetal state. As far as healthy subjects are concerned, maternal self-perceived stress, anxiety or depression is mirrored in maternal but not in fetal autonomic tone.