Abortion and preterm birth of foals are major reasons for reproductive losses in the horse. Risk pregnancies require close supervision so that adequate treatment can be initiated in time. The aim of this study was to determine normal values in heart rate (HR) and heart rate variability (HRV) of the pregnant mare compared to her foetus and to detect physiological changes during ongoing gestation. In mares, the RR interval decreased from 1480 ± 29 ms on day 270 of pregnancy to 1190 ± 58 ms on day 330 of pregnancy (p < 0.05). In contrast, foetal RR interval increased during the same time period from 611 ± 23 ms on day 270 of gestation to 756 ± 25 ms on day 330 of gestation (p < 0.05). Concomitantly, maternal HR increased and foetal HR decreased. No further changes in RR interval occurred during the last 10 days before foaling, neither in the mare nor the foetus. In the last hours preceding parturition, maternal RR interval was lower than at all times earlier in pregnancy (average of 1037 ± 13 ms) but did not change during this time. Maternal HRV did not change during gestation. Marked changes in HRV occurred only during the last minutes of foaling. Then, all HRV variables increased significantly (standard deviation of beat-to-beat interval: p = 0.01, root mean square of successive beat-to-beat differences: p < 0.01). The cardiovascular system of pregnant mares adapted to the demands of ongoing pregnancy with an increase in HR. We have no evidence that in healthy mares, pregnancy is a major stressor.