Background and Objectives: The gut microbiota plays a role in acquisition of nutrient and energy regulation. As it helps in calories extraction from ingested diet and facilitate storage of these calories in adipose tissue. Bacterial lipopolysaccharide (LPS) derived from gut microbiota acts as a trigger for chronic metabolic endotoxemia and systemic inflammation and this leads to development of obesity and insulin resistance. This study aims to identify the predominant gut flora in obese Egyptian children and its relation to the degree of obesity. Methodology: This was a case-control study included 20 obese and overweight children according to the International Obesity Task Force (IOTF) criteria. And 20 age and sex-matched healthy children with normal body mass index as control group. They were 22 males (55%) and 18 females (45%) whose mean age was 8.6±1 years. All cases that were on antibiotic in last three months were excluded. Clinical evaluation was done for all participants including full dietetic history. Full anthropometric measures and laboratory workup included stool culture for anaerobic bacteria (clostridia, bacterioids, bifidobacteria and lactobacilli) at enrollment for all participants were done. Results: There is statistical significant increase in Clostridia counts of Cases in comparison to control (p= 0.001) but, there was No statistical significant difference between the studied groups (P>0.05) with regard to Bifidobacteria, Bacteroids and lactobacilli. Also there is positive relationship between BMI and Clostridia colony count (P=0.024). Conclusion: There is association between increased gut clostridia (Firmicutes) and obesity in Egyptian children. However no relationship between type of gut flora and the degree of obesity, so determination of the role of the gut microbiota in childhood obesity may help to find new modalities for obesity management.