Aim The aim was to monitor the engraftment patterns and outcome of the graft by quantitative lineage chimerism testing based on short tandem repeats (STR), focusing on a longitudinal analysis post allogeneic myeloablative (MA) and nonmyeloablative (NMA) hematopoietic stem cell transplantation (HSCT). Methods The study was conducted on a cohort of 45 patients who received an allogeneic HSCT. All grafts were from a HLA ‘full house’ matched related donor. Post-transplant peripheral blood samples were collected from the recipient at D + 21, D + 30, D + 60, D + 90, D + 120, D + 180 and D + 365. Whole blood mononuclear cells was fractionated into CD3+, CD15 + and CD56 + cells using magnetic beads with sequential positive selection before extracting DNA. Sixteen STR (microsatellite) loci (D8S1179, D21S11, D7S820, CSS1PO, D3S1358, THOI, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, Amelogenin, FGA and D5S818) were amplified by multiplex PCR and the amplicon resolved on DNA sequencer. Results Post-transplant at D + 21 the percentage of donor T-cell chimerism was 100% in 17.9% cases whereas, the myeloid and NK cell donor chimerism was found to be 65% and 47.3% respectively. Overall the NK cell chimerism pattern closely approximated myeloid cell chimerism, while T cell recovery was distinctly different. In the MA category the donor chimerism reached >90% earlier than the NMA group. At D + 21 in the MA cohort, the average percentage of donor cells in CD3+, CD56+, CD15 + lineages was 84.12%, 93.92% and 97.61% whereas in the NMA cohort it was 79.4%, 85.7% and 90.99% respectively. The donor chimerism in MA group at D + 90 was >97% in all lineages, whereas in NMA group the donor cells in the three lineages were CD3 90.5%, CD56 92.8% and CD15 98.9%. The percentage of CD15 cells was higher at all-time points as compared to CD56 and CD3. In relapse the T cell chimerism showed maximum variation while myeloid cells demonstrated a more stable graph. No definite chimerism pattern was detected in the three lineages in ac GVHD. Conclusions This study establishes that, longitudinal chimerism testing is an important parameter for surveillance of engraftment and provides important information on disease recurrence or graft loss in HSCT. As a monitoring approach, it exploits the ability of the STR technique to compare numerical results between samples.