Deep-seated Candida infections and invasive aspergilloma are becoming a serious problem for individuals who need intensive care. The laboratory diagnosis of such infections is sometimes delayed due to relatively slow growth of these yeasts from clinical specimens. Several studies seem to indicate that early detection of deep-seated and invasive fungal infections is possible using genomic amplification methods. In the present study, we used a novel PCR assay that can assay five clinically common species (C. albicans, C. parapsilosis, C. tropicalis, C. glablata, and A. fumigatus) simultaneously. We evaluated the utility of this PCR based diagnosis with seven patients with candidiases. This assay is more sensitive than the culture result in 26 clinical samples (chi(2)=5.16, p < 0.05). In the clinical course of each patient, the number of detected fungal species gradually increased. More than two species were detected from single or several clinical specimens, and these patients would die within 14 days compared with the 61 day period individuals with zero or one species would live (p < 0.005). Before super infections of fungus, an antifungal drug could be applied to a suspected patient in the ICU. To improve sensitivity of this diagnosis from blood samples, we evaluated them after one day incubation at 34 degree. We found a PCR product in 10 of 20 blood samples taken from five children after bone marrow transplantation. One of four negative samples became positive after more than 48 hours of incubation.