Current research has shown that gut microbiota may play a fundamental role in neurological activity, behavior, mood, cognition, and possibly for the onset as well as the severity of autism spectrum disorder (ASD). Previous studies emphasized the possible correlation between Clostridium spp., gut colonization, and possible development or exacerbating of ASD in affected children. The aim of the present study was to investigate how Clostridia gut colonization can have an impact on the neurological outcome and anthropometric values in ASD children. The present study included 60 children (30 ASD and 30 neurotypical controls) of both sexes aged from 2 to 8 years. Children with ASD were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition (DSM-5), Autism Diagnostic Interview-Revised (ADI-R), as well as the Childhood Autism Rating Scale (CARS). Quantitative real-time polymerase chain reaction (real-time PCR) was used to determine Clostridium presence in the stools of the enrolled subjects. The number of Clostridium spp. (Clostridium paraputri, Clostridium bolteae, and Clostridium perfringens) found in the stools of ASD children was greater than neurotypical children. Children with ASD had two types of Clostridium (Clostridium diffiicile and Clostridium clostridiioforme) not found in neurotypical children, whereas neurotypical children yielded only one species (Clostridium tertium) not found in the ASD children. The present study emphasizes the potential correlation between gut colonization of Clostridia and the probability of developing or exacerbating ASD among Egyptian children. If Clostridium bacteria play a potential role in the etiology of ASD, this may open the possibility for effective treatment of these patients.