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The increasing use of probiotics in neonates deserves scrutiny of the therapeutic as well as potentially harmful effects of these bacteria. In this review we describe the possible application of probiotics in the more common diseases in the neonatal period.Recent advances in our capability to identify microbes and their function in the gastrointestinal tract offer exciting opportunities to discover the pathophysiology of enigmatic diseases such as necrotizing enterocolitis (NEC) and late-onset sepsis (LOS) in the neonate. The relationship of the resident intestinal microbes to neural and muscular processes such as intestinal motility and neurodevelopment are also being evaluated.We focus on the possibility of the application of probiotics for disorders of motility in the infant, NEC and LOS. Here we will summarize some of the recent advances in these areas as they relate to clinical practice and discuss areas where additional research is needed.