Background: Bone marrow transplantation (BMT) is considered as a curative therapy for a broad range of diseases. However, complications such as relapse and graft versus host disease (GVHD) may be observed following BMT. Chimerism analysis serves as a reliable indicator of transplant outcome. Complete chimerism refers to the complete replacement of hematopoietic system by donor cells, while mixed chimerism is the coexistence of both donor and recipient cells. The current study aimed to assess the relationship between molecular chimerism and GVHD as well as relapse and survival after allogenic hematopoietic stem cell transplantation (allo-HSCT) using Short Tandem Repeat-Polymerase Chain Reaction (STR-PCR). 
Material and Methods: This retrospective survival study was performed on 30 patients (Median age: 11.57±6.83 years) including 12 (40%) children with acute leukemia (6 patients (50%) acute myeloid leukemia and 6 patients (50%) with acute lymphoblastic leukemia patients). All patients received allo-HSCT during 2012-2016 at Montaserie Hospital, Mashhad, Iran. Chimerism analysis by STR-PCR method was carried out at cancer molecular pathology research center of Qaem hospital, Mashhad, Iran. Chimerism was assessed using 7-STR markers on recipients’ bone marrow aspiration samples on day 14 or 15 after BMT.
Results: The findings indicated that the mean chimerism level in patients with skin GVHD was significantly different compared to cases without skin GVHD (P=0.02). It was also found that patients’ survival was significantly longer in cases with complete chimerism (P=0.04).
Conclusion: Chimerism analysis may permit early prediction and monitoring of post-transplant complications such as GVHD, transplant rejection, and relapse and assist clinicians to proceed with suitable treatment plans.