Background: Establishment of the intestinal flora in childhood is a critical window for growth and development. Objective: The aim of the current meta-analysis is to investigate the composition, development of intestinal flora in children and its change with certain pathologies. Material and methods: A comprehensive search was conducted in Scopus, PubMed, Google Scholar and Other engines. A total of 603 articles were identified of them only 11 fulfilled our inclusion criteria. Results: Composition of the intestinal flora in children: Firmicutes (51.1%) and Bacteroidetes (36%) at the phylum level. Bacteroidaceae, Lachnospiraceae (17.5%) and Ruminococcaceae (13.9%) at family level. Bacteroides, Prevotella, Faecalibacterium and Bifidobacterium (16%, 8.69%, 7.51%, and 5.47%, respectively) at genus level. Children with cystic fibrosis had different intestinal microbiota structures compared to healthy children. Alterations of the intestinal microbiota could be a predisposing factor for the multi-systemic inflammatory syndrome. In SARS CoV-2: Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Verrucomicrobia (51%, 25%, 12%, 9%, and 2%, respectively). In non-diabetic children: Enterococcus 28.4%, and in children with type 1 diabetes Enterococcus 22.8%. The diversity and stability of the microbial composition: Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria, Fusobacteria, and Verrucomicrobia are different in diabetic and non-diabetic children. The percentage of microbiota species in children with signs of constipation varies compared to children without constipation. In children and adults, there is variation in species composition at the family, phylum, and genus level. Bacteroidetes raised in the severe autistic group. Dysbiosis was elevated in autistic children compared to healthy children. Sutterella sequences were absent in healthy children. Conclusion: It is a very important to know the influence of the change in the microbiota predisposition to develop different pathologies or the opposite, which opens a wide range in this subject, hence the importance of carrying out more in-depth studies and research, especially in childhood. Keywords: