The majority of chronic myeloid leukaemia (CML) patients express either e13a2 or e14a2 BCR-ABL1 transcripts. Variant fusion genes can arise, usually due to alternative splicing of either BCR or ABL1 exons, with molecular monitoring by quantitative PCR (qPCR) in response to tyrosine kinase inhibitor therapy rarely reported in such cases. A case of CML is described in which an e13a3 BCR-ABL1 fusion was characterised. A qPCR methodology was developed and applied prospectively to demonstrate a favourable molecular response to imatinib treatment. This case serves to highlight the requirement for molecular monitoring of those CML patients harbouring the e13a3 and other variant BCR-ABL1 transcripts.