We studied whether cerebral blood pressure autoregulation and kidney and liver injuries are associated in neonatal encephalopathy (NE). We monitored autoregulation of 75 newborns who received hypothermia for NE in the neonatal intensive care unit to identify the mean arterial blood pressure with optimized autoregulation (MAP ). Autoregulation parameters and creatinine, aspartate aminotransferase (AST) and alanine aminotransferase (ALT) were analyzed using adjusted regression models. Greater time with blood pressure within MAP during hypothermia was associated with lower creatinine in girls. Blood pressure below MAP related to higher ALT and AST during normothermia in all neonates and boys. The opposite occurred in rewarming when more time with blood pressure above MAP related to higher AST. Blood pressures that optimize cerebral autoregulation may support the kidneys. Blood pressures below MAP and liver injury during normothermia are associated. The relationship between MAP and AST during rewarming requires further study.