Objective: The aims of this study were to assess the prognostic significance of WHO-based Prognostic Scoring System (WPSS) in myelodysplastic syndrome (MDS) from a single center institute and to compare WPSS with the international prognostic scoring system (IPSS).Methods: A total of 100 cases with de novo MDS were reviewed and their karyotypes were detected. All of them were followed up and classified according to IPSS and WPSS risk groups. SPSS 13.0 software was applied to deal with all the data. The statistical methods included Kaplan - Meier, Log-rank test and cox regression.Results: Multivariate cox regression analysis indicated that WHO Classification (P=0.0190), karyotype abnormalities categorized according to IPSS (P=0.0159) and red blood cell (RBC) transfusion (P=0.0009) were the three most important independent factors for predicting overall survival (OS) of MDS. WPSS and IPSS both had great capacity in predicting the OS of MDS at the time of diagnosis (P