Excess or deficiency of natural trace elements has been implicated in the etiology of autism. This study explores whether concentration levels of toxic metals in the hair of children with autism significantly differ from those of age- and sex-matched healthy controls. In-hair concentration levels of antimony, uranium, arsenic, beryllium, mercury, cadmium, lead and aluminum from 40 boys with autism and 40 healthy boys were determined by Perkin-Elmer mass spectrometry. The children with autism had significantly (p < 0.001) higher in-hair concentration levels of lead, mercury and uranium. There was no significant difference between the two groups in the other five toxic elements. The ratio between nutritional elements and toxic metals among children with autism was within the normal range. The possible sources of the toxic metals are discussed. Such testing is informative but at present the practical implications in terms of diagnosis and clinical management are limited.