Lactoferrin (LF) is a natural component of human milk with antimicrobial, immunostimulatory and immunomodulatory properties. Several in vitro studies suggest that LF could promote an environment in the gut of neonates that favors colonization with beneficial bacteria. However, clinical studies on the correlation between the concentration of LF in breast milk and feces of infants and the gut microbiota in infants are lacking. In our study we analyzed the content of LF and the microbiota of breast milk and feces of infants of 48 mother-infant pairs (34 full-term and 14 pre-term infants) at birth and 30 days after delivery. In the term group, a significant decrease of mean LF concentration between colostrum (7.0 ± 5.1 mg/ml) and mature milk (2.3 ± 0.4 mg/ml) was observed. In pre-term group, breast milk LF levels were similar to those observed in full-term group. Fecal LF concentration of healthy infants was extremely high both in term and pre-term infants, higher than the amount reported in healthy children and adults. In term infants mean fecal LF levels significantly increased from birth (994 ± 1,828 μg/ml) to 1 month of age (3,052 ± 4,323 μg/ml). The amount of LF in the feces of 30 day-old term infants was significantly associated with maternal mature milk LF concentration (p = 0.030) confirming that breast milk represents the main source of LF found in the gut of infants. A linear positive correlation between colostrum and mature milk LF concentration was observed (p = 0.008) indicating that milk LF levels reflect individual characteristics. In pre-term infants higher mean concentrations of fecal LF at birth (1,631 ± 2,206 μg/ml) and 30 days after delivery (7,633 ± 9,960 μg/ml) were observed in comparison to full-term infants. The amount of fecal bifidobacteria and lactobacilli resulted associated with the concentration of fecal LF 3 days after delivery (p = 0.017 and p = 0.026, respectively). These results suggest that high levels of fecal LF in neonates, particularly in the first days of life, could represent an important factor in the initiation, development and/or composition of the neonatal gut microbiota. Since early host-microbe interaction is a crucial component of healthy immune and metabolic programming, high levels of fecal LF in neonates may beneficially contribute to the immunologic maturation and well-being of the newborn, especially in pre-term infants.