Cytarabine (ara-C) is the most effective agent for the treatment of acute myeloid leukaemia (AML). Aberrant expression of enzymes involved in the transport/metabolism of ara-C could explain drug resistance. We determined mRNA expression of these factors using quantitative-real-time-PCR in leukemic blasts from children diagnosed with de novo AML. Expression of the inactivating enzyme pyrimidine nucleotidase-I (PN-I) was 1.8-fold lower in FAB-M5 as compared to FAB-M1/2 (P ¼ 0.007). In vitro sensitivity to deoxynucleoside analogues was determined using the MTT-assay. Human equilibrative nucleoside transporter-1 (hENT1) mRNA expression and ara-C sensitivity were significantly correlated (r p ¼ À0.46; P ¼ 0.001), with three-fold lower hENT1 mRNA levels in resistant patients (P ¼ 0.003). hENT1 mRNA expression also seemed to correlate inversely with the LC 50 values of cladribine (r p ¼ À0.30; P ¼ 0.04), decitabine (r p ¼ À0.29; P ¼ 0.04) and gemcitabine (r p ¼ À0.33; P ¼ 0.02). Deoxycytidine kinase (dCK) and cytidine deaminase (CDA) mRNA expression seemed to correlate with in vitro sensitivity to gemcitabine (r p ¼ À0.31; P ¼ 0.03) and decitabine (r p ¼ 0.33; P ¼ 0.03), respectively. The dCK/PN-I ratio correlated inversely with LC 50 values for gemcitabine (r p ¼ À0.45, P ¼ 0.001) and the dCK/CDA ratio seemed to correlate with LC 50 values for decitabine (r p ¼ À0.29; 0.04). In conclusion, decreased expression of hENT1, which transports ara-C across the cell membrane, appears to be a major factor in ara-C resistance in childhood AML.