A retrospective comparison of WT1 and BCR-ABL1 expression was performed in 40 imatinib-treated chronic myeloid leukaemia patients. The overall correlation of WT1 and BCR-ABL1 was low. In two patients WT1 expression was increasing despite very low BCR-ABL1 levels. As both revealed Ph-negative aberrant clones, a second independent cohort of 20 cases, all with Ph-negative clonal evolution, was analysed. High WT1 expression (5.0-177.0%) was detected in a case with +11 and in four of eight cases with +8, but not in cases with del(20q) or -Y. Thus, increasing WT1 levels in molecular responders may indicate Ph-negative clonal cytogenetic evolution during imatinib treatment.