This retrospective study investigates the kinetics of bone marrow CD3+ (BM) chimerism evaluation by real time PCR (qPCR), in relationship with graft versus host disease (GVHD), relapse and mortality, post hematopoietic stem cell transplantation (HSCT). Chimerism studies were done at one or two consecutive time points.A quantitative real time PCR (qPCR, Celera)) method (0.1-0.05% sensitivity) was used to assess chimerism in 60 AML (acute myelogenous leukemia) patients who received myeloablative regimen prior to HSCT. BM CD3+ cell subsets were separated by autoMACS method (Miltenyi) and used for chimerism studies at 2 consecutive time points: median day 34 (27-47) and 103 (55-200).One time point study showed no differences in occurrence of aGVHD (acute) or relapse in 2 groups of patients with increasing percentage of recipient BMCD3+ (0-1% versus 1.01-10%). However, a previous one time point donor chimerism study had confirmed that patients with mixed donor chimerism were 47% less likely to develop aGVHD compared to patients with full donor chimerism (p=0.06). The second time point study showed that the recipient BMCD3+ % increased in 22 patients (37%) versus a decrease in 38 (63%). In recipients with increasing patient BMCD3+, the incidence of cGVHD (chronic) was 36%; Relapse and mortality were 32% and 18%, respectively. When recipient BMCD3+ decreased, the incidence of cGVHD increased to 45%, relapse and mortality decreased to 5% and 13%. GVHD and relapse were not detected in the 9% of the first and 27% of the 2nd cohort.Serial monitoring of HSCT chimerism by real time PCR may prove to be a useful adjunct to post-transplant management. Larger study groups are required to demonstrate the significance of post-transplant monitoring by qPCR.