Candida species are the leading cause of invasive fungal infections in children admitted to hospital. However, few data exist with regard to the clinical features, risk factors and prognosis for candidemia in neonates. The present retrospective study included 40 neonates from the Affiliated Children's Hospital of the Capital Institute of Pediatrics (Beijing, China) in the time period between January 1, 2006 and December 31, 2010 (candidemia group, n=19; non-candidemia group, n=21). The clinical characteristics, prognosis and previously identified risk factors for the two groups were recorded. According to the forward stepwise multivariate logistic regression analysis, administration of antibiotics >2 weeks prior, the use of glycopeptide antibiotics, maternal candidal vaginitis and secondary gastrointestinal surgery were identified as predictors of candidiasis. When compared with the non-gastrointestinal dysfunction group, the proportion of neonates that had been subjected to parenteral nutrition, central venous catheters, gastrointestinal surgery, secondary gastrointestinal surgery, repeated tracheal intubation and glycopeptide antibiotic administration was significantly higher in the gastrointestinal dysfunction group (P<0.05). Long-term application of antibiotics, use of glycopeptide antibiotics, maternal candidal vaginitis and secondary gastrointestinal surgery appeared to be the risk factors of candidemia in neonates. The neonates co-existed with gastrointestinal dysfunction suffering from candidemia were likely to experience growth retardation at 6 months after hospital discharge. Candidemia is potentially life-threatening situation for neonates, and if patients do not succumb it may affect their early development. © 2015, Spandidos Publications. All rights reserved.