BACKGROUND: The risk of obesity among autism spectrum disorder (ASD) children is high which could be related to a disorder in their metabolism. Brain derived neurotrophic factor (BDNF) is involved in metabolic control, language behavior, and intellectual development. Serotonin has a role in satiety and energy expenditure. AIM: Therefore, the aim of this study was to measure the serum levels of BDNF and serotonin in obese compared to non-obese ASD children. The influence of obesity on ASD severity, intellectual, and language development was also investigated. METHODS: The study included 60 autistic children (Group I: 30 ASD children with obesity and Group II: 30 ASD children without obesity). The serum BDNF and serotonin levels were estimated by ELISA and by high-performance liquid chromatography. RESULTS: All participants manifested delayed language development. Almost all of them had intellectual disability. The difference between groups regarding ASD severity, language, and intellectual development was non-significant. However, BDNF level in obese group was less than that in the other group while serotonin was higher in the obese group with significant statistical difference. CONCLUSION: The difference between the groups regarding the levels of BDNF and serotonin, which are involved in the brain development, could be related to obesity. The influence of obesity on ASD severity, intellectual, and language development of ASD children was not distinctive in the participants. The influence of such markers on ASD severity and cognitive performance needs further investigations.