Polymerase chain reaction (PCR) is a powerful and rapid method for specifically detecting BCR-ABL rearrangement by amplification of the complementary DNA (cDNA) produced by reverse transcription of BCR-ABL mRNA. We studied 29 patients for detecting the presence of BCR-ABL transcripts before and after bone marrow transplantation (BMT). Our sample was composed of two different groups of patients: one group (n = 18) was studied by serial follow-ups before and after BMT; a second group (n = 11) was studied several years after BMT. Detection of BCR-ABL was carried out with different primer sets at different periods of the clinical outcome of chronic myeloid leukaemia (CML). A comparison of PCR data and clinical-haematological conditions showed clear differences between patients. In the first group, eight patients showed a positive correlation between a favourable clinical outcome and molecular remission. Conversely, in the second group, six patients were BCR-ABL positive between 20 and 117 months after BMT, while only two of these patients showed signs of clinical relapse. Among all patients whose isoforms were known at some time during the course of CML, the more frequent isoform was b3a2. These results were compared to previous findings in the literature on diagnosis, outcome and prognosis of CML.