Elucidation of the aetiology and effective treatment of neurodevelopmental disorders is one of the challenges today. In this metallomics study for 2,550 children with autistic disorders aged 0–15 years, we demonstrate a remarkable molybdenum overload correlated to zinc deficiency. Histogram of scalp hair molybdenum concentration was log-normal distributed with the geometric mean of 62.0 ng/g (ppb), and 921 individuals (36.1 %) were found to have high molybdenum concentrations over 72.0 ppb that is the +2 S.D. threshold level in the reference range. In particular, the incidence rate of molybdenum overload in the infantile group aged 0–3 years was estimated 54.0 % (430 in 797) in male and 62.6 % (92 in 147) in female. Higher molybdenum concentrations over 116 ppb of the +3 S.D. level were detected at the rate of 18.7 and 21.8 % in male and female infant group aged 0–3 years, respectively. Interestingly, a high significant inverse relationship between molybdenum and zinc concentration (r = −0.510, p < 0.0001) was observed, with no significant association between molybdenum and copper (r = 0.058, p > 0.05). These findings suggest that the molybdenum overload in the children with autistic disorders is closely associated with zinc deficiency and maybe contributes to the aetiology of the neurodevelopmental disorders. We hope that evidence-based supplementation of the deficit minerals to individual leads to a precision intervention/treatment of the children with neurodevelopmental disorders.