Seven antisense oligodeoxynucleotides were selected using RNA structure 3.7 software and the principle of low overall ΔG (free energy). Their effects on cell growth, VEGF protein expression and apoptosis in HL60 and K562 leukemic cells were examined, and cell numbers and viability were assessed using trypan blue dye exclusion, MTT, ELISA and flow cytometry. The results showed that six of the seven antisense sequences inhibited the cell growth and down-regulated VEGF protein expression significantly. Endogenous VEGF plays an important role in the proliferation of HL60 and K562 leukemic cells. RNA structure software provides a rapid and efficient way of identifying effective antisense oligodeoxynucleotides.