To study the microbial flora of neonates admitted to neonatal intensive care units (NICUs) and the relationship of these flora with pathogenic microorganisms in cases of neonatal sepsis, this study was performed on 100 neonates admitted to NICU of Cairo University Hospitals.Specimens were collected from skin, upper respiratory tract and rectum of neonates and studied microbiologically.Surveillance was done on days 1 and 3 to detect infection in these children.Results showed the prevalent microorganisms were Staph coagulase-negative and Gram-negative bacilli. High agreement was found between the types of microorganism colonizing these neonates and the microorganisms isolated from infectious sites.