Autism spectrum disorder (ASD) has become a global public health concern, impacting the quality of life. The question of gene-environment interaction in the emergence of ASD remains a subject of ongoing debate, and exploring its pathophysiology is thoroughly related to metals as a risk factor. Therefore, this study aims to assess the levels of toxic (Al, Cd, Hg, and Pb) and essential (Cr, Mn, Fe, Ni, Cu, Zn, and Se) elements in toenail samples collected in children with ASD and neurotypical children, by ICP-MS. Parallelly, we will discuss the use of toenails as an exposure indicator. The study involved 208 children aged 3 to 14 from Marrakech, Morocco. One hundred two were diagnosed with ASD and 106 were neurotypical children. Significant statistical differences in the concentration of Cr, Mn, and Fe were documented between the two groups. Higher levels of Pb in toenails compared to reference values have been reported. No association was established between concentrations of elements and age. Spearman correlation coefficients revealed a significantly different pattern of mutual dependence for toxic and essential elements between the two groups. The strongest positive correlations were found in the neurotypical group (Fe-Mn (ρ = 0.750), and Se-Zn (ρ = 0.800)). These results provide additional, although inconclusive, evidence on the probable role of element disturbance in the pathogenesis of ASD. Further studies should be performed to explore other nutritional, cultural, sociodemographic, environmental, and methodological factors that may impact the levels of these elements in the nails and their possible correlation with the incidence of ASD.