The intestinal microflora has a significant role in intestinal health and gut function. The neonatal population is unique in that intestinal colonization is not established and is known to be influenced by delivery method, feeding, gestational age, and medical interventions. The preterm infant is particularly sensitive to colonization patterns as inherent intestinal defense mechanisms are immature and immature intestinal epithelial cells are known to have exaggerated inflammatory responses to both commensal and pathogenic bacteria. These responses contribute to the development of neonatal necrotizing enterocolitis in this patient population. As certain bacteria are known to influence intestinal maturation and down-regulate intestinal inflammation, it has been suggested that influencing the intestinal flora of preterm infants may be beneficial. Clinical studies indicate that probiotic therapy may decrease the incidence of necrotizing enterocolitis and studies are ongoing to elucidate the mechanism of action of different probiotic organisms. Although concerns remain and further study is necessary, probiotics are a plausible means of optimizing intestinal colonization and influencing outcome of these vulnerable infants.