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 intational 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<0.0001). In time-dependent analysis, WPSS can predict the OS accurately in the following three years after diagnosis (P<0.0001), while IPSS failed to predict the OS 24 months after diagnosis (P=0.1094).Conclusion: Our single center results proved that WPSS is a dynamic prognostic system which can predict the OS of MDS patients at any time during the course of their disease. This time-dependent prognostic scoring system may replace the IPSS in the near future.