Patients with CML post allogeneic BMT or during treatment with Interferon were monitored in bone marrow and peripheral blood for BCR-ABL transcripts by RT-PCR and in the majority of cases also by Southern blotting. Bone marrow and peripheral blood samples were obtained simultaneously and tested by RT-PCR with the objective to determine the usefulness to follow CML patients by testing peripheral blood rather than bone marrow samples. For the purpose of this study we have considered the test results obtained from bone marrow samples as the standard. A total of 111 CML patients were examined who underwent either an allogeneic BMT (n=91) or were treated with Interferon (n=20) amounting to a total of 163 assessments for BCR-ABL. Concordance of results was observed in 153 samples (93.9%). 10 samples showed discordance. Seven of these were subjected to repeat testing by RT-PCR. The previously obtained discordant results were confirmed. The sensitivity of peripheral blood assays was calculated to be 96.2% with a specificity of 89.5%. RT-PCR results restricted to Southern blot negative patients showed concordance of bone marrow and peripheral blood in 91.1% of tested samples with a sensitivity of 92.7% and a specificity of 88.6%. The subset of patients in which Southern blot testing was not available showed concordance at a similar level. Complete concordance was seen in all patients that were found to be positive by Southern blotting. We conclude from this study that peripheral blood testing for BCR-ABL transcripts by RT-PCR is a test with high sensitivity and specificity and may potentially replace bone marrow testing. This approach will probably result in a high level of acceptance by patients and may permit more frequent monitoring.