Childhood and adolescent onset obesity has reached epidemical proportions worldwide. Recent evidence suggests that obesity is associated with phylogenetic changes in the gut microbiota, which could potentially reveal new avenues for obesity prevention and treatment. A vast number of variables are influencing the gut microbial ecology and though many are proposed, the exact physiological processes behind the relationship are yet to be revealed. This review is focusing on recent advances addressing the potential role of the human gut microbiota in childhood and adolescent onset obesity.