Background: Disproportional heavy metals and essential elements were reported in children with autism spectrum disorder (ASD) that is obscure in etiology. Inevitably, the association is biased by diet and environmental factors. Methods: Fifty pairs, one with ASD and the other living together from the same special school with cerebral palsy (CP), were recruited in Hangzhou (China), aged from 2 to 11 years old (74.0 % male). All samples were divided into two subgroups: preschool-aged (2-5 years old) and school-aged (6-10 years old). Heavy metals (As, Hg, Pb) and essential elements (Al, Ca, Cu, Mg, Mn, Zn) in hair were quantified by inductively coupled plasma mass spectrometry analysis and flame atomic absorption spectroscopy. Results: The children with ASD generally had lower hair levels of Mn (ASD 0.124 mu g/g, CP 0.332 mu g/g, P = 0.001) compared to the children with CP. After stratification for age, there were no significant differences detected in preschool-aged group. In school-aged group, the results exhibited the children with ASD had higher hair Pb (1.485 mu g/g, 0.690 mu g/g, P = 0.007) and Cu/Zn ratio (0.092, 0.060, P = 0.003), while hair Hg (0.254 mu g/g, 0.353 mu g/g, P = 0.016)?Mn (0.089 mu g/g, 0.385 mu g/g, P = 0.002)?Mg (17.81 mu g/g, 24.53 mu g/g, P = 0.014) and Zn (100.15 mu g/g, 135.83 mu g/g, P = 0.007) showed an opposite pattern. Conclusions: These results suggest an imbalance of Mn in Chinese children with ASD.