Isolated sulfite oxidase deficiency is a rare genetic neurometabolic disease. The first symptoms of this disorder (similar to symptoms of ischemic events) may lead to misdiagnosis and to subsequent birth of affected children in these families. This study characterizes the magnetic resonance (MR) imaging and (for the first time, to our knowledge) the MR spectroscopy features of isolated sulfite oxidase deficiency to provide a means for early and correct diagnosis. Three patients with isolated sulfite oxidase deficiency are studied who manifested intractable seizures and severe hypotonia in the immediate postnatal period with an unknown diagnosis, despite extensive workup. MR imaging and proton MR spectroscopy examinations were performed early in the neonatal period in 2 infants and after 5 months in the third infant. The prominent MR features were early cystic white matter damage, accompanied by profound cerebral atrophy in the third infant. Compared with hypoxic-ischemic disorder, MR findings in isolated sulfite oxidase deficiency demonstrate a more severe condition, without subsequent recovery. The MR spectroscopy studies indicate early onset of energetic and metabolic imbalance. Urine stick findings demonstrated high sulfite levels in 2 patients, and the final diagnosis was subsequently made based on molecular, biochemical, and genetic findings. Magnetic resonance imaging and MR spectroscopy measurements may help differentiate isolated sulfite oxidase deficiency from hypoxic-ischemic condition in patients in whom this diagnosis is not clinically suspected and may lead to further genetic antenatal inquiry that might prevent the birth of other infants affected with this severe and incurable congenital disease.