Autism is a disease of variable clinical manifestation, genetically predisposed and depending on various epigenetic factors. Magnesium plays an important role among those factors. The study, involving 93 autistic children, demonstrated a significant reduction of tissue magnesium levels, high homocysteine levels and normal blood serum magnesium levels. Magnesium deficiency causes a reduced methylation of homocysteine to methionine; and high homocysteine level causes reduction of genome transcription and synaptic plasticity – being base irregularities in autism. The study results indicate purposefulness of determination of hair magnesium in autistic children, confirm usability of homocysteine determination as a part of a diagnostic process, and constitute the basis for attempted treatment of autistic children with magnesium products