In the present study, an atypical case of chronic myeloid leukemia (CML) in a 32-year-old male was reported. CML cases with e13a3 breakpoint cluster region (BCR)-ABL transcripts are extremely rare. Reverse transcription quantitative‑polymerase chain reaction (RT-qPCR) was initially negative due to the primer corresponding to ABL a2 sequences and diagnosis was based upon analysis of the bone marrow smear, fluorescence in situ hybridization and karyotype analysis. RT‑qPCR analysis with the ABL primer, which was located in ABL exon 3 to enable the detection of fusions with either ABL a2 or exon a3 demonstrated the presence of the BCR‑ABL fusion transcript e13a3. The patient responded well to Nilotinib and achieved a complete cytogenetic response after 3 months.