Background:  Trillions of microbial cells in the human body are thought to be vital to human survival. Microbial cell populations are at maximum density within the intestinal compartment, referred to as the gut microbiota. Aim: To describe the neonatal microbiota in hospitalized preterm patients and to detect the relation between necrotizing enterocolitis (NEC), sepsis and preterm gut microbiota. Patients and methods: This was a prospective study on preterm very low birth weight neonates. Rectal swabs were collected at postnatal weeks one, two and three. The Illumina MiSeq system was employed to sequence the 16S rRNA gene. Results were compared to that of routine blood culture and were correlated with the use of antimicrobials. Results: Rectal swabs of the first week had predominantly no organisms (89.7%). Klebsiella genus was the most predominant bacteria in all rectal swabs (5.8%, 22.0%, 22.0% of the 1^st, 2^nd and in 3^rd swabs results respectively). In spite of the non-significant results on the level of number of operational taxonomic unit (OTU) and chao indices, the association of microbiota change with NEC and sepsis could not be excluded. The significant organisms at phylum level in NEC and sepsis groups was Proteobacteria. There was no significant correlation between change of antibiotic therapy and results of rectal swabs at the 1^st, 2^nd and 3^rd weeks. Conclusion: The gut of preterm neonates born by CS who received antibiotics was mostly sterile at first week. Subsequent colonization by pathogenic organisms such as Klebsiella and Enterobacter occurred after the first week.