Abstract Background Autism spectrum disorder (ASD) is a category of neurodevelopmental disorders characterized by social and communication impairment and restricted or repetitive behaviors. Aim of the Work to estimate the quantity of Candida in autism spectrum disorder (ASD) patients compared to normal children and to find the association between Candida colony count and severity of ASD. Patients and Methods The study was carried out on 40 children, diagnosed as autism and 40 normal children as control group recruited from Pediatrics and adolescent Psychiatric Clinic at Ain Shams University Pediatrics Hospitals and Main Microbiology lab in Clinical Pathology Department of Ain Shams University. The study was conducted on a wide age group ranging from 3 to 14 years, (mean age of 6.30±2.40 years), Stool sample was collected from each patient in a sterile container, cultured on Sabouraud Dextrose Agar (SDA) and colony count was determined. Identification of isolated Candida species was done using chromogenic media. Results The study revealed statistically significant difference in Candida isolation rate among patient and control group with p-value (p = 0.006). Candida species were isolated from 23 patients (57.5%) and from 10 child in control group (25%), But detected that stool count was nonsignificant in severe autistic group compared to mild to moderate autistic group with p-value more than 0.05 NS. There were 14 patients (60.9%) with C. Albicans; 2 patients (8.7%) C. Glabrata; 6 patients (26.1%) C.Krusie and one patient (4.3%) C. Utilis, among candida species. Conclusion ASD is more common among male than female; ratio about 4:1. The high rate of intestinal colonization by Candida species in ASD children may represent a part of syndrome related to immune system disorders that may play a role in the pathogenesis of ASD. C. albicans was the predominant isolate than other non-Candida albicans species in ASD. The degree of candida colonization represented as quantitative colony count is not related to the severity of CARS among ASD patients.