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The presence of the Philadelphia chromosome (Ph) in chronic myelogenous leukaemia (CML) is a specific cytogenetic change resulting from a reciprocal translocation between chromosomes 9 and 22. In 5–10% of newly diagnosed cases there are variant translocations (vPh) involving more chromosomes. This paper presents the case of a CML patient with a complex variant translocation involving chromosomes 1, 6, 9, 17 and 22. A molecular analysis did not reveal any mutation in the kinase domain of BCR-ABL1 gene or the mutation of TP53 gene. After the first-line treatment with imatinib no cytogenetic or molecular response was obtained. The change of treatment to dasatinib resulted in a minimal cytogenetic response (minCyR) followed by a minor cytogenetic response (mCyR). The application of nilotinib in the third-line treatment resulted in a complete molecular response (CMolR) and therapy success. The likely reason for the failure of the first- and second-line treatment was the loss of a fragment of the 17p13 region as a result of a variant translocation. The change can be a functional equivalent of the loss of one copy of TP53. The analysis of presented case confirms the significance of the detailed evaluation of the composition of vPh complex variant translocations as well as importance of combination cytogenetic and molecular diagnostics in CML treatment monitoring. It makes possible to adequate diagnose higher-risk patients and apply effective treatment strategies if an aberration is identified. [ABSTRACT FROM AUTHOR]