Background: Autism Spectrum Disorder usually presents in early childhood with qualitative abnormalities in social interactions, noticeably affected communication skills, and restricted repetitive and stereotypic behaviors. Evidence has led to the hypothesis that autistic children may be at increased risk for being overweight or obese. Aim of the study: This study aims to assess obesity and its correlation with Lactobacillus and Bifidobacteria in stool of autistic children compared to healthy controls. Methods: This case-control study was conducted in the Learning Disability and Neurological Rehabilitation Clinic, National Research Centre on 30 autistic children, aged from 5 to 8 years compared to 30 healthy children who were age and sex matched. Autistic children were diagnosed according to DSM-5 Diagnostic Criteria for autism, Childhood Autism Rating Scale (CARS) and Gilliam Autism Rating Scale (GARS). Body Weight (Wt), Body Height (Ht), Body circumferences (Head, Neck, Waist, Hip, Mid-upper arm), Skin fold thicknesses (Biceps, Triceps, Subscapular, Suprailiac) were measured. Body Mass Index (BMI Wt/Ht2 ) was calculated. Stool Real-time PCR was done to evaluate the Lactobacillus and Bifidobacteria. Results: There is a statistically significant difference in body weight, BMI, waist circumference, supra-iliac skinfold thickness (<0.05) and neck circumference (<0.001) and Z scores of body weight, BMI, waist, hip, mid upper arm circumferences and sub-scapular and supra-iliac skinfold thicknesses (<0.05) and neck circumference (<0.001) being higher in autistic children than control ones. The Lactobacillus and Bifidobacteria in stool of autistic children are less abundant than the control group with a statistically significant difference (<0.05). There is no correlation between the Lactobacillus and Bfidobacteria concentrations and the different anthropometric parameters among the autistic children. European Journal of Molecular & Clinical Medicine ISSN 2515-8260 Volume 07, Issue 11, 2020 4094 Conclusion: The increased incidence of obesity in autistic children isn’t related to gut dysbiosis. It could be attributed to their restricted physical activities and serious eating problems.