The antisense drug synthesized by DNA synthesizer is an oligodeoxynucleotide (ODN). The purity of the drug should be determined effectively. Because the ODNs are molecules with negative charges at pH 12, they can be separated according to the quantity of charges with them on the ion-exchange column. On anion exchange column, MONO-Q, the ODNs ranged from 19 bases to 21 bases can be separated successfully by gradient elution of NaCl solution from 0 mol/L to 1.8 mol/L. The experiment proved that the fast protein liquid chromatography is a very useful tool for the determination of the antisense drug.