The worldwide prevalence of obesity and associated metabolic syndrome (MetS) has increased threefold over the last five decades. Among children, this trend is alarming due to the premature onset of MetS. The data regarding how the structure and composition of gastrointestinal (GIT) microbiota either promote or attenuate obesity and MetS are limited. Objectives: We carried out this study to investigate the relationship between microbial profiles and diagnosis of MetS among children with obesity. Fifty subjects with a diagnosis of obesity or Mets were enrolled. We collected clinical information, demographic data, dietary records, and stool specimens. Overall, there was no significant difference in the diversity of GIT microbiota between the two subgroups of children with obesity or MetS. We also found no differences in the diversity of GIT microbiota between the sexes and blood pressure categories. However, we observed a significant difference between the structure, composition, and diversity of the gut microbiome when the subjects were stratified using a BMI cut-off of 30. Subjects with a BMI ≥ 30 had a lower abundance of Bacteroidetes and a greater abundance of Actinobacteria and Firmicutes compared to those with a BMI value of less than 30. This gut microbiota signature is more like the GIT microbiome profile of adults with obesity and may represent accelerated changes among children. Additional studies are needed to investigate the role of obesity in the maturation of gut microbiota in children with morbid obesity.