This study investigated microbiological, clinical, and management issues and outcomes for Danish fungemia patients. Isolates and clinical information were collected at six centers. A total of 334 isolates, 316 episodes, and 305 patients were included, corresponding to 2/3 of the national episodes. Blood culture positivity varied by system, species, and procedure. Thus, cases with concomitant bacteremia were reported less commonly by BacT/Alert than by the Bactec system (9% [11/124 cases] versus 28% [53/192 cases]; P < 0.0001), and cultures with Candida glabrata or those drawn via arterial lines needed longer incubation. Species distribution varied by age, prior antifungal treatment (57% occurrence of C. glabrata, Saccharomyces cerevisiae, or C. krusei in patients with prior antifungal treatment versus 28% occurrence in those without it; P = 0.007), and clinical specialty (61% occurrence of C. glabrata or C. krusei in hematology wards versus 27% occurrence in other wards; P = 0.002). Colonization samples were not predictive for the invasive species in 11/100 cases. Fifty-six percent of the patients had undergone surgery, 51% were intensive care unit (ICU) patients, and 33% had malignant disease. Mortality increased by age (P = 0.009) and varied by species (36% for C. krusei, 25% for C. parapsilosis, and 14% for other Candida species), severity of underlying disease (47% for ICU patients versus 24% for others; P = 0.0001), and choice but not timing of initial therapy (12% versus 48% for patients with C. glabrata infection receiving caspofungin versus fluconazole; P = 0.023). The initial antifungal agent was deemed suboptimal upon species identification in 15% of the cases, which would have been 6.5% if current guidelines had been followed. A large proportion of Danish fungemia patients were severely ill and received suboptimal initial antifungal treatment. Optimization of diagnosis and therapy is possible.