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The interaction between Wilms tumor gene 1 (WT1) and the promoter region of the multidrug resistance-1 (MDR1) gene has been previously reported but the clinical significance of the coexpression of WT1 and MDR1 in acute lymphoblastic leukemia (ALL) is still largely unknown. In this study, the expression levels of WT1 and MDR1 mRNA in 57 adult ALL patients were simultaneously detected using multiplex fluorescence real-time quantitative polymerase chain reaction. The expression levels of WT1 and MDR1 in bone marrow samples of adult ALL patients were significantly higher than those in the normal samples (P<0.001), and in addition, the expression levels of WT1 and MDR1 mRNA were highly correlated (r(s)=0.404, P=0.002). According to the expression levels of these two genes, the patients in this study were subdivided into the following three groups: low-WT1/low-MDR1 (n=16), high-WT1 or high-MDR1 (n=24), high-WT1/high-MDR1 (n=17). There was no significant difference in response to induction therapy among these three cohorts (P=0.217). The overall first year relapse rate was 53.2% (25 out of 47 ALL patients). High-WT1/high-MDR1 mRNA expression was strongly associated with BCR-ABL expression and a higher tendency to be T-cell ALL type. In addition, high-WT1/high-MDR1 have a significantly higher relapse rate (P=0.048) and shorter disease free survival (P=0.016). Our data suggests that high-WT1/high-MDR1 levels of mRNA expression may be associated with relatively poorer outcomes in patients with ALL. Therefore, the expression of WT1 and MDR1 may provide useful information for clinical decision.