The aim of this study was to analyze the hematopoietic chimerism after non-myeloablative allogeneic peripheral blood stem cell transplantation (NAPBSCT). 28 patients received NAPBSCT were evaluated. The conditioning regimen included FBC (fludarabine, busulphan, cyclophosphamide) +/- Ara-C. Peripheral blood was collected before and after transplantation in different periods. Semi-quantitative assessment of hematopoietic chimerism was performed by short tandem repeat-polymerase chain reaction (STR-PCR), polyacrylamide gel electrophoresis (PAGE) and silver staining, and analyzed by Image Analysis System. The results showed that on day 30 after transplantation, one patient failed to engraft, but 22 cases formed complete chimerism (CC) and 5 cases were of mixed chimerism. On day 7 after transplantation, the average percentage of donor cells was 74.71%. The time of dominance of the donor-specific allelic pattern preceded the recovery time of neutrophils and platelets. The incidence of aGVHD in group CC was significantly higher than that in group MC (P < 0.05). There was no significant difference in the incidence of cGVHD and disease relapse between group CC and group MC (P > 0.05). One patient relapsed in CC status without a transitional stage of MC. One patient with MC rejected grafts in early stage. 3 patients with MC transferred to CC and got complete remission after early implementation of therapy. It is concluded that sequential and quantitative detection of chimerism may be of great value to evaluate engraftment and to predict graft rejection, disease relapse and GVHD. Furthermore, it may provide a basis for early intervention treatment in the related complications.