Abstract Background and Objectives The co-existence of recipient’s and donor’s hematopoietic systems after allogeneic marrow transplantation is called mixed chimerism. Chimerism analysis provides a national method of assessing the ability of different conditioning regimens, graft-versus-host disease (GVHD), prophylactic regimens, and cellular therapy to promote engraftment. Materials and Methods The association of mixed chimerism with acute graft-versus-host disease (GVHD), disease recurrence, survival, and relapse free survival was investigated in 91 patients 12 and 79 of whom underwent either bone or peripheral blood HLA-identical marrow transplantation respectively. Chimerism was assessed using multiplex amplification of shorty tandem repeats (STR-PCR). Cases included thalassemics (19 subjects), AML (29), ALL (20), CML (18) and others (5). Median age was 21 (age range of 3-50). There were 38 females (41.8%) and 53 males (58.2%). Conditioning was busulfan plus cyclophosphamide in 34 patients, busulfan plus fludarabin in 51 patients and busulfan plus fludarabin plus anti-thymocyte globulin in 6 patients. Median time of follow up was 13 months. Data was analyzed using SPSS statistical software. Results On day 30 after transplantation, mixed chimerism (MC) was observed in 15 patients (16.5%), complete donor chimerism (CC) in 72 patients (79%), and no chimerism in 4 patients. The incidence of acute GVHD was significantly lower in mixed chimeras than in complete chimeras (p=0.01) but there was no significant difference in acute GVHD grade (I, II vs. III, IV) between two groups. The incidence of relapse and overall survival were 17.6% and 88.9% respectively showing no significant difference between MC and CC. Relapse free survival was 80.2% and not significantly different between two groups. Conclusions Despite some previous reports, we found no significant difference in survival and relapse rate between MC and CC. Key words: Allogenic, Bone Marrow Transplantation , Chimerism, PCR |