Background: Neonates are born sterile, but many parts of their bodies are colonized by various microorganisms thereafter. The neonatal period is important for the colonization of microflora in the intestines, which is influenced by various factors including the type of delivery mode and feeding. We investigated the effects of the delivery mode and feeding type on the dynamics of gut microbiota in healthy Korean newborns. Methods: One hundred ninety-two healthy term neonates of birth weights which were adequate for gestational age were included in this study. Fecal specimens from newborns were collected at time points of 1 days, 3 days, 7 days, and 14 days after birth. Microbiological composition was examined by next-generation sequencing (NGS) of Illumina MiSeq® system. Comparative analysis was performed composition, alpha and beta diversity of newborns fecal microbiota at the same age across four time points from day 1 to day 14 of age. We also investigated the difference of microbiota composition according to delivery mode and feeding type at the genus levels. Results: At phylum level, Proteobacteria species were decreased and Actinobacteria species were increased across four time points from day 1 to day 14 of age. At genus level, streptococcus and Escherichia/shigella species were decreased and Bifidobacterium species were increased across four time points from day 1 to day 14 of age. Shannon and Simpson index diversity of alpha diversity were both increased across four time points. The MDS plot of beta diversity at four time points showed a big change on the day 14 from the change on the day 3 and 7. According to delivery mode, cesarean-delivered newborns have higher levels of harmful bacteria, while vaginal-delivered newborns have higher levels of beneficial bacteria. We performed a cluster analysis by dividing by feeding type. There was a big difference between bifidobacterium and Esherichia/shigella between breastfeeding and formula feeding. Conclusions: The results of this study show that the diversity of gut microbiota according to days after birth and the impact of delivery mode and feeding type on the dynamics of gut microbiota profiles in Korean newborns.