PURPOSE: This study aimed to investigate the influence of routine probiotic supplementation on causes of neonatal morbidity and mortality, such as necrotizing enterocolitis (NEC) and late onset sepsis. METHODS: All neonates born at <32 weeks of gestation and weighing <1,500 g admitted to the neonatal intensive care unit during the study period were included. The study period was divided into the pre-probiotic period, between January 2009 and February 2011, and the probiotic period, between November 2012 and December 2014. The probiotic given was a mixture of Lactobacillus plantarum, L. rhamnosus, Bifidobacterium lactis and B. longum, administered at the time of the first feeding over 2 mL once daily. RESULTS: A total of 358 infants were screened for enrollment, with 149 infants included in the pre-probiotic group (mean birth weight 937 g, mean gestational age 27.9 wk), and 158 in the probiotic group (1,040 g, 28.6 wk). Probiotics had no statistically significant impact on NEC and late onset sepsis. However, three cases of probiotic related sepsis occurred after the infants were routinely administered probiotics in our unit. CONCLUSION: Routine probiotic supplementation did not reduce the incidence of NEC in very low birth weight (VLBW) infants. However, severe sepsis was caused by strains in the probiotic administered to patients. Therefore, routine prophylactic use of probiotic in VLBW infants should be performed cautiously.