Background & Aims. The diagnosis of chronic myeloid leukemia (CML) is confirmed in case of translocation t(9;22) (q34;q 11 ) is revealed by chromosomal banding analysis and/or BCR-ABL fusion gene transcript is detected by reverse-transcriptase polymerase chain reaction (RT-PCR). However, rare types of chimeric BCR-ABL transcript have been described and they may be overlooked. Moreover, timely CML diagnosing and detection of different types of BCR-ABL transcript are very important task, because the clinical course of the disease and efficacy of the therapy with tyrosine kinase inhibitors partly depend on the structure of BCR-ABL fusion. In some cases CML may be diagnosed without the chromosomal banding analysis and be confirmed by RT-PCR alone, so we consider it important to develop a diagnostic algorithm that allows to detect virtually all types of BCR-ABL fusion gene transcript. Methods. Over the period from January, 2004, till December, 2013, in the Molecular biology laboratory of Pediatric oncology and hematology center in Regional Chlildren’s Hospital # 1 (Yekaterinburg), the diagnosis of CML was confirmed in 1082 patients: 531 (49 %) males and 551 (51 %) females. The median age was 50 years (range 5-88 years). Chromosomal banding analysis and nested RT-PCR were performed in all patients. Reverse primers for nested RT-PCR are localized in exons 2 and 3 of ABL and are used for detection of all types of BCR-ABL transcript. Forward primes for typical e13a2 and e14a2 (M-bcr) transcripts are localized in exons 12 and 13 BCR gene, forward primes for e1a2 (m-bcr) transcript are complementary to exon 1 of BCR. While atypical amplicons are detected we performed Sanger sequencing with primers of the second round of RT-PCR and BigDye Terminator 3.1 kit. Results. Based on 1082 of confirmed CML cases we have developed a diagnostic strategy for detection of typical and atypical types of BCR-ABL fusion gene transcript in CML patients using RT-PCR. Proposed algorithm allowed to detect typical BCR-ABL transcript, e14a2 and e13a2, in 62.53 % and 35.89 % of cases, respectively. Atypical transcripts, e13a3, e14a3, e19a2, e1a2, e3a2, e6a2, and e8a2, were detected in 1.57 % of cases. Conclusion. Therefore, the proposed diagnostic algorithm proved to be effective for detection of typical and atypical types of BCR-ABL fusion gene transcripts in CML patients.