Therapeutic hypothermia is standard of care in management of moderate/severe hypoxic-ischemic encephalopathy. Persistent pulmonary hypertension of the newborn is associated with hypoxic-ischemic encephalopathy and is exacerbated by hypoxemia and hypercarbia. Gas exchange is assessed by arterial blood gas analysis (with/without correction for body temperature), pulse oximetry, and end-tidal CO2. A retrospective chart review. Regional perinatal center in Western New York. Fifty-eight ventilated neonates with indwelling arterial catheter on therapeutic hypothermia. None. We compared pulse oximetry, PaO2, end-tidal CO2, and PaCO2 during hypothermia and normothermia in neonates with hypoxic-ischemic encephalopathy using 1,240 arterial blood gases with simultaneously documented pulse oximetry. During hypothermia, pulse oximetry 92-98% was associated with significantly lower temperature-corrected PaO2 (51 mmHg; interquartile range, 43-51) compared with normothermia (71 mmHg; interquartile range, 61-85). Throughout the range of pulse oximetry values, geometric mean PaO2 was about 23% (95% CI, 19-27%) lower during hypothermia compared with normothermia. In contrast, end-tidal CO2 accurately assessed temperature-corrected PaCO2 during normothermia and hypothermia. Hypothermia shifts oxygen-hemoglobin dissociation curve to the left resulting in lower PaO2 for pulse oximetry. Monitoring oxygenation with arterial blood gas uncorrected for body temperature and pulse oximetry may underestimate hypoxemia in hypoxic-ischemic encephalopathy infants during whole-body hypothermia, while end-tidal CO2 reliably correlates with temperature-corrected PaCO2.