We performed a two-step polymerase chain reaction (PCR) to detect bcr-abl-specific mRNA in 440 peripheral blood and/or bone marrow samples of 30 chronic myeloid leukemia (CML) patients (mean 15, range 2-50 samples) following non T-cell-depleted allogeneic (n = 28) or syngeneic (n = 2) bone marrow transplantation (BMT). Median follow-up after BMT is 40 months (range 2-116 months), the median observation time 29 months (range 2-40 months). In 15 patients (50%), bcr-abl-specific mRNA could be detected following BMT. Bcr-abl positivity was rare in patients who were in hematological remission for at least 40 months (2/11). In five patients, PCR positivity was observed only once; all five patients are in complete hematological remission. Ten patients showed bcr-abl specific mRNA in two or more consecutive samples. Hematological relapse occurred in five of the latter patients. Bcr-abl positivity preceded hematological relapse in all cases. Bcr-abl positivity was detected more frequently in patients without graft-versus-host disease (GVHD) (11/15), than in patients with GVHD (4/15) (p < 0.02). Our data indicate that transient bcr-abl positivity is not usually followed by hematological relapse, while patients, who are positive in serial samples have a high risk of relapse.