Background:  Allogeneic Hematopoietic Stem Cell Transplantation (allo-HSCT) is used as treatment of choice for patients with acute myeloid leukemia (AML). We aimed to evaluate the prognostic factors in 2-year overall survival of patients with non-M3 AML who underwent allogenic HSCT.
Methods: This is a Cross sectional retrospective study. Demographic data and study of variables such as age, sex, complete remission status, Karnofsky performance status scale at baseline and at time of transplantation, occurrence of GVHD (acute and chronic), relapse and 2-year survival were extracted from records of 49 patients who underwent allogenic HSCT from years 2006-2013 at BMT center in Imam Khomeini Hospital. All Autologous SCTs and M3 cases were not included. All data were analyzed with SPSS software. P<0.05 was considered as statistically significant. 
Results: The overall survival rate was 55% in the patients. There was no significant difference in overall survival between complete remission (CR) 1 and CR2. Relapse rate was 6%. Mean 2-year Karnofsky scale was 93.7. Mean admission time following BMT was 22 days which was significantly related to 2-year performance status (P=0.02). Admission complication rate was 22.5% (GVHD 12%). Rate of overall GVHD was 55%, 40% of whom developed chronic GVHD which had a positive effect on 2-year overall survival (OS2).The patient’s first performance state (K1) had a significant correlation with 2-year performance state (P<0.05) and OS2 (P<0.05). 
Conclusion: Chronic GVHD and initial Karnofsky performance status scale can be considered as good prognostic factors in patients with AML who undergo allo-HSCT.