Hypoxic ischemic encephalopathy affects ~5/1000 neonates and causes neonatal death and 2-year disability. Using neonatal MRI to predict neonatal and 2-year outcomes remains a key open question. However, expert scoring of neonatal MRI, the current norm, only focuses on a few key brain regions based on subjective clinical experience. We objectively and comprehensively examined the associations with neonatal and 2-year outcomes throughout the brain. Our new findings – many voxels, subregions and fibers that are not considered in expert scoring systems, with a left hemisphere dominance, were associated with outcomes – provide new knowledge for future individualized outcome prediction.