In vitro amplification of polymorphic genetic markers, especially short tandem repeats (STRs), has become standard laboratory practice in the monitoring of allogeneic bone marrow transplant patients. After initial analysis of donor and recipient samples at multiple loci before transplantation, one or more loci are used to follow engraftment status in subsequent specimens. We describe an unusual pattern of STRs in a transplanted patient with a prior history of refractory acute myelogenous leukemia. DNA chimerism studies showed a lack of engraftment at 1 and 2 months after transplantation. Atypical minor peaks occurred at each of three STR loci in the pre-transplant and 2-month post-transplant recipient samples. However, these peaks were of equal amplitude as the major corresponding allele in the 1-month post-transplant sample. A history of myelodysplasia with specific chromosomal deletions before the patient's acute myelogenous leukemia diagnosis appears to explain the spurious peaks. STR analysis of blood and archival paraffin-embedded tissues collected from the patient at various time points before transplantation reflected the evolution, progression, and response to therapy of the myelodysplasia. The case illustrates the need for comprehensive evaluation of pertinent clinical and laboratory data during engraftment monitoring to identify potential sources for error in interpretation of STR analysis.