Changes in the composition of antimicrobial peptides and antibacterial activity in the intestine during the early postnatal period, strongly influenced by external factors such as breastfeeding and the mode of delivery, have been described in humans. The aims of our study were to describe the time course of calprotectin (C) human beta defensins type 2 (hβd2) and tumor necrosis factor-α (TNF-α) excretion in stools of term newborns (TN) and preterm newborns (PN) during the first weeks of their life and to improve our understanding on the factors influencing their excretion. We longitudinally evaluated the fecal values of calprotectin, hβd2 and TNF-α in 233 stool samples from PN and TN, in relation to the mode of delivery, gestational age (GA) and type of feeding. No significant differences in the levels of any of the three factors were found in relation to the mode of delivery or feeding type. Calprotectin, hβd2 and TNF-α were influenced only by GA. Further studies are needed to get better insight into the development of the gastrointestinal mucosal immune system in newborns.