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We report the CSF and plasma amino acid concentrations and their ratios in a male patient with arginase1 deficiency with an unusual early presentation at 34 days of age. He developed hyperammonaemic coma (ammonia >400 μmol/L; normal <90 μmol/L) on postnatal day 35. CSF and plasma concentrations were assayed by ion-exchange chromatography on day 36. Arginine was increased both in plasma (971 μmol/L; controls (mean ± 2SD) 50 ± 42) and in CSF (157 μmol/L; controls 19 ± 8.6), resulting in a normal CSF/plasma ratio of 0.16 (controls 0.41 ± 0.26). Interestingly, glutamine was disproportionately high in CSF (3114 μmol/L; controls 470 ± 236) but normal in plasma (420 μmol/L; controls 627 ± 246); the ratio exceeded unity (7.4; controls 0.76 ± 0.31). The CSF/plasma ratios of most neutral amino acids were elevated but not those of the imino- and of the dibasic amino acids lysine and ornithine. The mechanism leading to the increase of most neutral amino acids in brain is not known.A normal glutamine in plasma does not exclude an increased concentration in CSF; it could be useful to ascertain by MRS that a high CSF glutamine concentration truly reflects a high concentration in brain tissue for better understanding its pathogenesis.