Autism is a neurodevelopmental disorder with unclear pathogenesis. Many clinical observations and hormone studies have suggested the involvement of the neuroprotective hormone ghrelin in autism. The current study aimed to investigate the potential role of ghrelin in autism and to elucidate the associated hormonal dysregulation. This case-control study investigated acyl ghrelin (AG), des-acyl ghrelin (DG), total testosterone (TT), free testosterone (FT), leptin and growth hormone (GH) levels in 31 male children with autism and 28 healthy age and sex-matched controls. Hormone levels were measured in the blood using enzyme-linked immunosorbent assay and chemiluminescence immunoassay kits. AG, DG and GH levels were significantly lower in the autism group than in the control group (p ≤ 0.001, p ≤ 0.005 and p ≤ 0.05, respectively). However, TT, FT and leptin levels were significantly higher in the autism group than in the control group (p ≤ 0.05, p ≤ 0.001 and p ≤ 0.01, respectively). Our results for the first time demonstrate low AG and DG levels in autistic children. Considering the capacity of ghrelin to affect neuroinflammatory and apoptotic processes that are linked to autism, this study suggests a potential role for the hormone ghrelin in the pathogenesis of autism.