The following changes were found in children in the minimal cerebral dysfunction: the hypoaminoacidemia and hypoaminoaciduria with decrease of glutamate and aspartate, their amides, methionine and serine in the blood and urine; decrease of lysine, taurine, tyrosine, catecholamines and serotonin in the blood; increase of GABA and glycine in the blood; increase of xanthurenate, proline and cysteine in the urine. The ratio excitatory/inhibitory mediatory amino acids decreased significantly. The ratio essential/nonessential amino acids and concentrations of amino acids, transporting by x-AG, beta and A/ASC systems, decrease in the blood; majority of transporting systems in the kidney functions augmently. Disturbances of amino acids metabolism disappear or decrease in successful treatment.