Polymorphisms of genes encoding enzymes involved in float metabolism have long been hypothesized to be maternal risk factors for autism. In addition to genetic background, the exposure to mercury whether organic or inorganic can give rise to the symptoms of autism spectrum disorders (ASD) such as impairments in social interaction, communication difficulties and repetitive behaviors and interests. Our objective was to investigate the association between metallothionein (MT) gene polymorphism and levels of mercury in the hair of Egyptian autistic children. Thirty-one autistic children diagnosed by DSM-IV (Diagnostic and Statistical Manual of Mental Disorders, 4^th Edition criteria) were subjected to hair mercury measurement using Atomic Absorption Spectrometry (AAS) and were compared to polymorphism of genes MT1A and MT1E matched healthy children. The present study revealed that there was a highly significant increase in the mean hair mercury level in autistic patients than controls (0.79±0.56) ppm vs. (0.13±0.08) P<0.001 associated with polymorphism in MT1A (AG genotype). There was high significant difference in MT1E (GG genotype) between males and females (P<0.001) while in control were non significant.The results of this study highly support the increase in the mean hair mercury level in autistic children compared to controls.