The plasmid DNA was purified using the Fractogel EMD TMAE (M) anion exchange media. The dynamic loading capacity of this media for plasmid DNA was 0.62 mg/mL. It was found that when the lysate of bacteria was incubated with either Triton X-114 or Triton X-100 before purification, the average content of endotoxin left in the purified plasmid DNA was 6.42 EU/mg or 9.50 EU/mg, respectively. These results were much lower than that without pre-incubation (67.82 EU/mg). The purification of plasmid DNA and the removal of endotoxin were achieved in one step using anion-exchange chromatography. This method is simple, fast and of low cost.