Childhood obesity is currently a major global health challenge affecting a growing proportion of pediatric patients. Increasing consumption of highly processed foods, excess calorie intake, and reduced physical activity are considered major contributing factors. In recent years, research has focused on other factors, one of which is the influence of gut microbiota composition. The purpose of our study was to summarize the current knowledge regarding the relationship between gut microbiota composition and metabolic diseases in the pediatric population. We searched the PubMed and Scopus databases, primarily for studies published between 2020 and 2026. The analysis showed that alterations in the composition of the gut microbiota have been reported in overweight or obese children with associated type 2 diabetes, type 1 diabetes, or hyperlipidemia. It was found that the composition of the gut microbiota also varies according to non-modifiable factors such as gender, age, and ethnicity. The limitations of the analyzed studies primarily include small research groups and the lack of consideration of coexisting diseases and other factors influencing the results. Despite these limitations, the evidence available indicates that the gut microbiota may contribute to the development and progression of obesity in children. Further research in this area is necessary to identify potential therapeutic approaches and preventive strategies targeting the gut microbiota and its composition in order to reduce the risk and progression of obesity in children.