PURPOSE: Long term hospitalized infants in neonatal intensive care units(NICUs) are prone to systemic infection. It is important to differentiate systemic candidiasis from systemic bacterial infection early in the course. Thus, in this study, we have compared clinical characteristics of systemic candidiasis and systemic bacterial infection, in premature low birth weight infants. METHODS: Retrospective chart review of the medical records of 20 patients with systemic candidiasis and 23 patients with systemic bacterial infection was performed. RESULTS: Among the risk factors of systemic candidiasis, total parenteral nutrition(TPN), the use of broad spectrum antibiotics, central catheter insertion, endotracheal intubation and the use of H2 blockers were more frequent in neonates with systemic candidiasis than neonates with systemic bacterial infection. Apnea with bradycardia developed more frequently in neonates with systemic candidiasis compared with systemic bacterial infection(75% vs 39%). In laboratory findings at symptom onset, seven cases(35%) of systemic candidal infections and two cases(9%) of systemic bacterial infections showed leukopenia and thrombocytopenia(P=0.03). Blood was the most frequent isolation site of candida and bacteria. CONCLUSION: In neonates with systemic candidiasis, apnea with bradycardia, pneumonia and thrombocytopenia were prone to develop more frequently. The use of TPN, antibiotics and central catheters was strongly associated with systemic candidiasis. Empirical treatment with antifungal agent should be considered in critically ill neonates with above findings.