Perinatal Hypoxic ischaemic injury is a significant cause of cerebral insult. The initial clinical evaluation is difficult. Blood testing and imaging studies are not always sufficient, and there is a need for early identification of newborns infant at risk. In vivo magnetic resonance spectroscopy can be used to assess cerebral metabolism. We have studied with proton magnetic resonance spectroscopy (1H MRS) and phosphorus magnetic resonance spectroscopy (31P MRS) three full term babies affected by perinatal hypoxia-ischaemia with more selective involvement of the basal ganglia. The outcome was good at 6 months in all the babies. We have calculated the ratio NAA/Cr, Cho/Cr, Lac/Cr and mI/Cr using PRESS TE 40, 135 and 270 sequences for 1HMRS with a 1.5 T Magnet Picker Eclipse. 31 P spectroscopy was also performed with ISIS sequences to calculate the intracellular pH. In all the three babies we have observed a very low ratio NAA/Cr in the basal ganglia and not in the white matter, corresponding at the more severe damage in the basal ganglia showed by MR imaging. This low ratio could mean a selective damage in basal ganglia with neuronal loss.