We evaluated the clinical usefulness of a polymerase chain reaction (PCR) assay amplifying the 18S ribosomal RNA gene of fungi for the diagnosis of deep candidiasis, compared with that of the β-glucan test or Cand-Tec test. Thirty critically ill patients who had received prolonged care with intravenous hyperalimentation and endotracheal intubation in the intensive care unit and were suspected of having deep fungal infections were examined. Twenty-one were fungi positive in the PCR assay (70%). Among 24 samples in which the PCR assay, β-glucan test and Cand-Tec test were performed simultaneously, 75% of the samples (18/24) were fungi positive in the PCR assay, whereas only 54% (13/24) had positive reactions in the β-glucan test and 21% (5/24) in the Cand-Tec test. The results of the Cand-Tec test showed no relationship with those of the PCR or β-glucan test. The lower limit of detection in the PCR assay was 4-5 CFU/ml of C. albicans in blood. No fungal organism was amplified from the serum of 20 healthy individuals. The results of the PCR assay and β-glucan test showed a significant correlation in this study, but the PCR assay proved to be more sensitive than the β-glucan test (p<0.05), and to be more useful for the clinical diagnosis and monitoring of deep Candidiasis.