A model of global hypoxia during Caesarean-section (C-section) birth has been widely used to study long-term effects of birth hypoxia on central nervous system (CNS) function. However, the actual degree of CNS and systemic hypoxia produced by the birth insult in this model has never been characterised. Additionally, the way in which the dam is anaesthetised during the C-section procedure may impinge on the degree of hypoxia experienced by the neonate. This study examined how a period of global birth anoxia and isoflurane/N2O anaesthesia interact to affect measures of CNS and systemic hypoxia in neonatal rats born by C-section compared with control, vaginally born animals. A 10-min period of global anoxia just before birth increased blood lactate, a metabolic indicator of systemic hypoxia, increased brain lactate and decreased brain ATP to a similar extent in pups born by C-section from either decapitated, unanaesthetised dams or dams anaesthetised with 2.5% isoflurane. Thus, this model does produce systemic and CNS hypoxia in the neonate. Pups born by C-section with a higher concentration of isoflurane (3.5%), in the absence of added global anoxia, also showed reductions in brain ATP at birth. In addition, 10 min of global anoxia produced greater increases in blood lactate in pups born from dams anaesthetised with the higher concentration of isoflurane. Thus, the concentration of anaesthetic used in this model may affect the degree of CNS or systemic hypoxia experienced by the neonate. Compared with vaginal birth, pups born by C-section with 2.5% or 3.5% isoflurane (and no added global anoxia) showed decreased PO2 and pH, and increased pCO2 in systemic blood taken <30 s after birth. Exposure to global anoxia during C-section birth actually increased systemic PO2 at <30 s after birth, presumably due to ventilatory responses to hypoxemia and hypercapnia; this effect of anoxia was reduced in anaesthetised compared with unanaesthetised pups. Thus, global anoxia acts as a stimulus for rapid recovery of systemic PO2 at birth, and this stimulus is dampened by isoflurane/N2O anaesthesia. These results should aid in understanding how CNS and systemic hypoxia at birth contribute to long-term changes in brain biochemistry and behaviour in this model.