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Thyroid hormones (TH) influence heart sympathetic control maturation but its effect on the vagal control is less clear. It is also unknown if early thyroid deficiency leads to altered vagal heart control in adulthood. We aimed to study changes in vagal heart control resulted from thyroid deficiency at various ontogeny stages. We used two hypothyroidism models: acute (AH, adult male rats drank 250 ppm propylthiouracil (PTU) for 4 wk) and maternal (MH, male offspring from dams drank 7 ppm PTU in gestation and 14 postnatal days). AH rats showed greatly depleted TH level. In MH model TH level was also reduced in 2-wk-old rats, but not changed in 10-wk-old rats. To assess heart control, we recorded ECG in awake rats. The intrinsic heart rate (HR after methylatropine (MA) and atenolol (AT) injections) was lower in AH and in 2-wk-old MH rats compared to respective controls. Despite euthyroid state, the intrinsic HR was also reduced in 10-wk-old MH. Resting HR was decreased in AH and in 2-wk-old MH rats and tended to be lower in 10-wk-old MH rats. AH rats showed smaller tachycardia in response to MA, similar distortion was seen in 10-wk-old MH rats. Thus, thyroid deficiency at any ontogeny stage results in HR decline along with reduced vagal tone. Even transient early HT is followed by the altered vagal heart control in the adulthood. Such long-term changes are clinically relevant due to prevalence of thyroid disorders in pregnancy.