Candida auris is a newly described species whose clinical significance is not clear. Here, we describe the first three cases of nosocomial fungemia caused by C. auris, which confirms that it is a causative agent of bloodstream infections. All three patients presented persistent fungemia for 10-31 days. The isolates obtained from the three patients were misidentified as Candida haemulonii and Rhodotorula glutinis by the VITEK 2 and the API 20C systems, respectively. C. auris was confirmed by sequence analysis of the internal transcribed spacer region and D1/D2 regions of the 26S ribosomal DNA of the rRNA gene. The minimum inhibitory concentration (MIC) ranges of amphotericin B (AMB), fluconazole (FLU), itraconazole, and voriconazole were 0.5-1, 2-128, 0.125-2, and 0.06-1 μg/ml, respectively. All isolates were susceptible to caspofungin (MIC = 0.06 μg/ml) and micafungin (MIC = 0.03 μg/ml). One patient developed breakthrough fungemia while receiving FLU therapy, and two patients who received FLU therapy followed by AMB showed therapeutic failure and fatal outcome. Our cases show that C. auris fungemia can be persistent despite FLU or AMB therapy, which emphasizes the importance of accurately identifying this species.