The establishment of the newborn's gut microbiota is a major physiological phenomenon and a critical period for the child's future health. The composition and complexity of the gut microbiota vary considerably among individuals and across different regions of the intestine. It is essentially composed of a diverse community of bacteria, forming a complex ecosystem that functions symbiotically with our body. The initial colonization of the newborn's intestine is influenced by several factors. There is compelling evidence that disruption of the normal colonization process can lead to alterations in the important symbiotic relationship required for immune homeostasis. For instance, neonates delivered via the cesarean section or exposed to excessive perinatal antibiotics exhibit inadequate initial colonization and aberrant mucosal immune function. Breast milk has an essential role on the establishment of the GM. It is an important source of commensal bacteria. The gestational age also plays a significant role in the establishment of the gut microbiota. In the case of premature delivery, an atypical gut microbiota is established, characterized by a lower diversity of bacterial species. In this review, we summarize recent literature concerning factors influencing the establishment of the gut microbiota.