Substantial characteristics of autism are cognitive and psychophysical disorders. Etiopathogenetic factors are thought to be responsible for development of autism in children with genetic predisposition as well as have their effect on the severity of the disorders. The main problem of early identification of patients affected by autism spectrum disorder is that there are no clear diagnostic criteria. The aim of our study was assessment of hair magnesium and serum homocysteine concentrations in children with autism. The presented work is a continuation of previous study in which we investigated the influence of disturbances in magnesium and homocysteine levels in children with autism, performed on a new, larger group of patients. One hundred and forty children had hair magnesium levels analyzed, as well as blood serum levels of homocysteine and magnesium. Hair magnesium analysis was performed using a flame atomic absorption spectrometer, blood serum homocysteine determination was performed using a radioimmunological method, and blood serum magnesium level was determined using a biochemical method. Our research showed normal magnesium blood levels and significantly high homocysteine levels and very low hair magnesium levels. Low concentration of hair magnesium progresses with age. Our hypothesis is that magnesium deficiency, as a relevant epigenetic factor, might be decreasing methylation of homocysteine, therefore decreasing genome transcription and lowering the synaptic plasticity. We suggest that analysis of hair magnesium and serum homocysteine levels might be useful in identification of children with autism spectrum disorder, as well as control of its treatment. Obtained results and performed analysis might therefore justify supplementation of magnesium among children with autism.