BACKGROUND: Allogeneic hematopoietic stem cell transplantation (HSCT) provides children with life-threatening conditions an opportunity for survival. Complications from graft-versus-host disease (GVHD) are a major source of morbidity and death, recently linked to gut dysbiosis in the hematopoietic stem cell transplantation (HSCT) population. But so far, no comprehensive study has been conducted to investigate this relationship in the children population. In this systematic study, we investigated the Gut microbiota variation and diversity and gut GVHD in pediatrics. METHODS: A systematic review according to PRISMA standards was performed from inception till August 2024. Out of 568 originally chosen publications, 10 studies involving 490 pediatric subjects satisfied the eligibility criteria and were included. RESULTS: The findings obtained from the study included in the present systematic study mostly indicated the use of combined treatments including Busulfan, Cyclophosphamide, and total body irradiation and in some studies the use of anti-thymocyte globulin and Melphalan as conditioning regimens. In addition, out of 10 reviewed studies, 9 reported a significant decrease in gut microbiota diversity following GVHD. However, in all studies, an increased variation was reported. So that most of the studies showed a decrease in the levels of beneficial bacteria and producers of short-chain fatty acid products in the intestine such as Ruminococcaceae and Enterococcus, which is also observed in the intestinal microbiota population of healthy people. CONCLUSION: As a result, our findings indicated a decrease in diversity as well as a change in intestinal microbiota in children with GVHD under HSCT in most of the studies.