BACKGROUND: The VITEK-2 yeast susceptibility test (AST-YS01; bioMerieux, Hazelwood, MO, USA) has recently been introduced as a fully automated, commercial antifungal susceptibility test system that determines MIC endpoints spectrophotometrically, thereby eliminating subjective errors. We compared the ATB FUNGUS 2 (bioMerieux) and VITEK-2 (AST-YS01) systems to the CLSI M27 method for susceptibility testing of Candida isolates. METHODS: We tested 59 Candida species that were isolated from blood cultures at Wonju Christian Hospital between September 2008 and August 2009. We compared MIC results for amphotericin B, flucytosine, fluconazole and voriconazole using the ATB FUNGUS 2 and VITEK-2 (AST-YS01) tests to those obtained by the CLSI M27 broth microdilution method. RESULTS: Within two-fold dilutions of MICs, the agreement of the ATB FUNGUS 2 and VITEK-2 (AST-YS01) tests with the CLSI method according to antifungal agents were: amphotericin B, 100% vs. 100% flucytosine, 100% vs. 100% fluconazole, 83.6% vs. 98.3% and voriconazole, 83.6% vs. 96.7%, respectively. The categorical discrepancies for fluconazole and voriconazole were 20.4% and 18.6% for ATB FUNGUS 2, and 6.8% and 0% for VITEK-2 (ASTYS01). There were no major errors for fluconazole and voriconazole in either ATB FUNGUS 2 or VITEK-2 (AST-YS01) tests. CONCLUSION: The VITEK-2 system (AST-YS01) appears to be rapid and highly correlative with the CLSI method, suggesting that it is effective for antifungal susceptibility testing for Candida species in clinical settings.