Although near-infrared spectroscopy is increasingly being used to monitor cerebral oxygenation in neonates, it has a limited penetration depth. The T₂-prepared Blood Imaging of Oxygen Saturation (T₂-BIOS) magnetic resonance sequence provides an oxygen saturation estimate on a voxel-by-voxel basis, without needing a respiratory calibration experiment. In 15 neonates, oxygen saturation measured by T₂-prepared blood imaging of oxygen saturation and near-infrared spectroscopy were compared. In addition, these measures were compared to cerebral blood flow and venous oxygen saturation in the sagittal sinus. A strong linear relation was found between the oxygen saturation measured by magnetic resonance imaging and the oxygen saturation measured by near-infrared spectroscopy ( R² = 0.64, p < 0.001). Strong linear correlations were found between near-infrared spectroscopy oxygen saturation, and magnetic resonance imaging measures of frontal cerebral blood flow, whole brain cerebral blood flow and venous oxygen saturation in the sagittal sinus ( R² = 0.71, 0.50, 0.65; p < 0.01). The oxygen saturation obtained by T₂-prepared blood imaging of oxygen saturation correlated with venous oxygen saturation in the sagittal sinus ( R² = 0.49, p = 0.023), but no significant correlations could be demonstrated with frontal and whole brain cerebral blood flow. These results suggest that measuring oxygen saturation by T₂-prepared blood imaging of oxygen saturation is feasible, even in neonates. Strong correlations between the various methods work as a cross validation for near-infrared spectroscopy and T₂-prepared blood imaging of oxygen saturation, confirming the validity of using of these techniques for determining cerebral oxygenation.