Therapeutic hypothermia is standard care for infants with moderate to severe encephalopathy. (1) H MRS thermometry (MRSt) measures regional brain absolute temperature using the temperature-dependent water chemical shift. This study evaluates the clinical feasibility of MRSt in human neonates, and correlates white matter (WM) and thalamus (Thal) MRSt with conventional rectal temperature (T(rectal) ) measurement. Fifty-six infants born at term underwent perinatal MRSt for suspected hypoxic-ischaemic brain injury and 33 infants born preterm had MRSt at a term-equivalent age; 56 of the 89 had T(rectal) measured after MRSt of either a Thal or posterior WM voxel, or both. MRSt used point-resolved spectroscopy (no water suppression; TR = 1370 ms; TE = 288 ms; 1.5 × 1.5 × 1.5 cm(3) Thal and 1.1 × 1.3 × 1.4 cm(3) WM voxels). Time domain data were phase and frequency corrected before summation and motion-corrupted data were excluded from further analysis using simple criteria [preprocessing + quality assurance (QA)]. Two published water temperature-dependence calibrations [both using cerebral creatine (Cr), choline (Cho) and N-acetylaspartate (Naa) as independent reference peaks] were compared. The temperature measurements derived from Cr, Cho and Naa were combined to give a single amplitude-weighted combination temperature (T(AWC) ). WM and Thal T(AWC) correlated linearly with T(rectal) (Thal slope, 0.82 ± 0.04, R(2) = 0.85, p < 0.05; WM slope, 0.95 ± 0.04, R(2) = 0.78, p < 0.05). Preprocessing + QA improved the correlation between WM T(AWC) and T(rectal) (R(2) increased from 0.27 to 0.78, p < 0.001). Both calibration datasets showed specific inconsistencies between the temperatures calculated using Cr, Cho and Naa reference peaks when applied to this neonatal dataset. Neonatal MRSt is clinically feasible. Preprocessing + QA improved MRSt reliability in WM. The consideration of MRSt calibration internal biases is necessary before combining MRSt temperatures from multiple reference peaks to obtain T(AWC) . Copyright © 2012 John Wiley & Sons, Ltd.