Since the outcomes of patients with candidemia is poor and Candida spp. with increased resistance to antifungal therapy may be associated with these results, the emergence of these blood infections caused by non-C. albicans Candida spp. was explored prospectively over a two-year period (2009-2010). Candidemia was defined as the recovery of Candida spp. in culture from a patient's blood sample. The in vitro susceptibility of each isolate to amphotericin B, caspofungin, fluconazole and voriconazole was determined. In addition, characteristics of patients and outcomes were investigated in real-time. The Candida distribution was compared to that observed in a similar study 10 years earlier in the same hospital. A total of 182 patients with candidemia were included in the study. While C. albicans was the most frequently isolated species (n = 102), non-C. albicans Candida spp. included; C. glabrata (n = 32), C. parapsilosis (n = 21), C. tropicalis (n = 13), C. krusei (n = 8), C. kefyr (n = 3), C. lusitaniae (n = 2), C. lipolytica (n = 2), C. famata (n = 1), C. guilliermondii (n = 1), C. inconspicua (n = 1), C. dubliniensis (n = 1), C. sake (n = 1) and C. nivariensis (n = 1). In seven patients, C. albicans was associated with another Candida spp. Surprisingly, this prospective study demonstrated that regardless of the department (intensive care unit or hematological department), Candida spp. distribution was no different from that found in the 1998-2001 survey, except for C. krusei. A reduction in the proportion of C. krusei isolates was observed from 2000-2010 (P = 0.028) as a result of its decreased recovery in the hematological department.