Previous studies have shown altered brain metabolism after cerebral hypoxia-ischemia, using magnetic resonance spectroscopy with echo times (TE) of 272 and 136 ms, based on peak-area or peak-height ratios. The present study examined the additional value of proton magnetic resonance spectroscopy with a short TE (31 ms) to predict a poor outcome in neonates with brain hypoxia-ischemia. Studies were performed in 21 full-term neonates with perinatal asphyxia in a 1.5 tesla magnetic field. Proton magnetic resonance spectroscopy was performed in a single volume of interest including the basal ganglia. TE of 272, 136 and 31 ms were used. After curve-fitting procedures, peak-areas as well as peak-height ratios of different brain metabolites were calculated, comparing patients with a poor versus a good outcome. Seven neonates out of 21 had a poor outcome. Neonates with a poor outcome showed a significantly lower N:-acetylaspartate/choline (NAA/Cho) and a significantly raised lactate/NAA (Lac/NAA) ratio using TE of 272 and 136 ms. Using a TE of 31 ms, no differences were found in glutamate/NAA (Glx/NAA), Glx/Cho, myo-inositol/NAA (mI/NAA), and mI/Cho ratios between neonates with a good and those with a poor outcome. Highest predictive values could be achieved for NAA/Cho with a TE of 136 ms. We conclude that low NAA/Cho and high Lac/NAA ratios predict a poor outcome in neonates with cerebral hypoxia-ischemia. TE of 272 and 136 ms have a better predictive value than a TE of 31 ms.