Although thymomas are relatively common mediastinal tumors, to date not only has a universal system of pathologic classification not been established but neither has a clearly defined predictable relationship between treatment and prognosis been made. Recently, a new guideline for classification was reported by WHO, and efforts, based on this work, have been made to better define the relationship between treatment and prognostic outcome. In the present study a comparative analysis between the WHO classification and Masaoka stage system with the clinical disease pattern was conducted. Material and Method: A total of 98 patients undergoing complete resection for mediastinal thymoma between Juanuary 1993 and June 2003 were included in the present study. The male female ratio was 48 : 50 and the mean age at operation was $49.6{\pm}13.9\;years.$ A retrospective analytic comparison studying the relationship between the WHO classification and the Masaoka stage system with the clinical disease pattern of thymoma was conducted. Pathologic slide specimens were carefully examined, details of postoperative treatment were documented, and a relationship with the prognostic outcome and recurrence was studied. Result: There were 7 patients in type A according to the WHO system of classification, 14 in AB, 28 in B 1, 23 in B2, 18 in B3, and 9 in type C. The study of the relationship between the Masaoka stage and WHO classification system showed 4 patients to be in WHO system type A, 7 in type AB, 22 in B 1, 17 in B2, and 3 in type B3 among 53 $(54{\%})$ patients shown to be in Masaoka stage I. Among 28 $(28.5{\%})$ patients in Masaoka stage II system, there were 2 patients in type A, 7 in AB, 4 in B 1, 2 in B2, 8 in B3, and 5 in type C. Among 15 $(15.3{\%})$ in Masaoka stage III, there were 1 patient in type B1, 3 in B2, 7 in B3, and 4 in type C. Finally, among 2 $(2{\%})$ patients found to be in Masaoka stage IV there was 1 patient in type B1, and 1 in type B2. The mean follow up duration was $28{\pm}6.8$ months. There were 3 deaths in the entire series of which 2 were in type B2 (Masaoka stages III and IV), and 1 was in type C (Masaoka stage II). Of the patients that experienced relapse, 6 patients remain alive of which 2 were in type B2 (Masaoka III), 2 in type B3 (Masaoka I and III) and 2 in type C (Masaoka stage II). The 5 year survival rate by the Kaplan-Meier method was $90{\%}$ for those in type B2 WHO classification system, $87.5{\%}$ for type C. The 5 year freedom from recurrence rate was $80.7{\%}$ for those in WHO type B2, $81.6{\%}$ for those in type B3, and $50{\%}$ for those in type C. By the Log-Rank method, a statistically significant correlation between survival and recurrence was found with the WHO system of classification (p<0.05). An analysis of the relationship between the WHO classification and Masaoka stage system using the Spearman correction method, showed a slope=0.401 (p=0.023), showing a close correlation. Conclusion: As type C of the WHO classification system is associated with a high postoperative mortality and recurrence rate, aggressive treatment postoperatively and meticulous follow up are warranted. The WHO classification and Masaoka stage system were found to have a close relationship with each other and either the WHO classification method or the Masaoka stage system may be used as a predict prognostic outcome of Thymoma.