Decreased heart rate variability (HRV) may be a biomarker of brain injury severity in neonatal hypoxic-ischemic encephalopathy for which therapeutic hypothermia is standard treatment. While therapeutic hypothermia may influence the degree of brain injury; hypothermia may also affect HRV per se and obscure a potential association between HRV and hypoxic-ischemic encephalopathy. Previous results are conflicting. This study aimed to investigate the effect of hypothermia on HRV in healthy, anaesthetised, newborn piglets. Six healthy newborn piglets were anaesthetised. Three piglets were first kept normothermic (38.5-39.0 degrees C) for 3 h, then exposed to hypothermia (33.5-34.5 degrees C) for 3 h. Three piglets were first exposed to hypothermia for 3 h, then rewarmed to normothermia for 3 h. Temperature and ECG were recorded continuously. HRV was calculated from the ECG in 5 min epochs and included time domain and frequency domain variables. The HRV variables were compared between hypothermia and normothermia. All assessed HRV variables were higher during hypothermia compared to normothermia. Heart rate was lower during hypothermia compared to normothermia and all HRV variables correlated with heart rate. Hypothermia was associated with an increase in HRV; this could be mediated by bradycardia during hypothermia.