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The Vitek MS matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) instruments was evaluated for the identification of yeast isolates.A total of 1058 yeasts were isolated from patients with invasive fungal infections (IFIs) from 23 hospitals in China between September 2010 and August 2011.All the isolates were sent to the microbial laboratory of Peking Union Medical College Hospital for analysis with the Vitek MS system, and sequencing of the internal transcribed spacer (ITS) regions of ribosomal DNA was used as the reference method.Among the 1058 isolates, 1023 (96.7%) isolates were correctly identified, while 2.5% of isolates were unidentified and 0.8% were misidentified.Considering the species included in database (1030 isolates), no IDs and mis IDs were obtained for 6 isolates (0.6%) and 1 isolate (0.1%), respectively.While as for the species absent in database, 71.4% had no identification and 28.6% got misidentifications.Above all, Vitek MS system performed well in identifying common clinical species.In conclusion, the Vitek MS system was proved to be an accurate and simple tool for the yeasts identification.