Our research aim was twofold; a) to determine if maternal physical activity during pregnancy would influence the development of fetal cardiac autonomic control and b) whether HRV could serve as a sensitive indicator of fetal programming effects. Pregnant women with singleton pregnancies participated in a longitudinal study. Magnetocardiograms (MCG) were recorded during pregnancy and when infants reached 1 month of age. Metrics of heart rate (HR) and variability (HRV) were calculated from the R-R intervals. Fetal HR was lower and HRV higher in the Exercise group and this effect persisted into the infant period. We conclude that maternal physical activity can influence the development of fetal cardiac autonomic control and this may give offspring an adaptive advantage.