We have identified novel BCR-ABL mRNA fusions by RT-PCR in two patients with Philadelphia (Ph) chromosome positive leukaemia. Sequencing revealed in-frame fusions consisting of part of BCR exon e8 spliced to ABL exon a2 in one patient and part of BCR exon e13 spliced to ABL exon a2 in the other. The breaks within BCR exons e8 and e13 did not conform to consensus splice sites, suggesting that the aberrant fusion mRNAs may have arisen as a result of translocation breakpoints at these sites. This was confirmed by genomic DNA bubble PCR for the second patient. These data show that BCR-ABL translocation breakpoints can occasionally occur within coding exons.