BACKGROUND: Infections are an important cause of morbidity and mortality in patients in intensive care units (ICUs). Fungal infections have increased substantially over recent years and fungi have become one of the important pathogens in ICU patients. This study tests the hypothesis that the incidence of fungal infections is lower in critically ill patients under mechanical ventilation receiving enteral rather than total parenteral nutrition. METHODS: By using a prospectively built database, we analyzed retrospectively the charts of 110 critically ill, intubated patients hospitalized in surgical and medical ICUs and receiving selective digestive topical decontamination (SDD), which consisted of administering non-absorbable antibiotics. Patients without contraindications, and expected to be intubated for more than 72 h, received enteral nutrition within 24 h after intubation. Patients with contraindications for enteral nutrition received total parenteral nutrition, which was discontinued when the criteria for enteral nutrition were met. The incidence of fungal infections in both subgroups of patients was compared. RESULTS: Seventy-nine patients received enteral nutrition and 31 total parenteral (10 patients did not meet the inclusion criteria). Both subgroups were similar with regard to their APACHE II score, age, sex distribution and comorbidities at the time of study entry. No difference was observed in the rate of fungal infections between enteral nutrition (5/29) and total parenteral nutrition (7/71) patient groups. CONCLUSION: No significant decrease in the incidence of fungal infections in critically ill patients receiving SDD was observed between those receiving enteral and total parenteral nutrition.