This work describes partial purification of three different DNA binding proteins, i.e. H-NS, RNA polymerase and Oct-1, using pre-packed HiTrap Heparin 5 ml columns in the initial chromatographic step. H-NS was purified directly from a bacterial lysate using heparin affinity chromatography and gel filtration as the only chromatographic steps. The protein was shown to be 70% pure by SDS-PAGE. RNA polymerase was purified using gel filtration and ion exchange chromatography after the heparin step. SDS-PAGE analysis showed the polymerase to be 90% pure. Recombinant human Oct-1 was shown to bind to HiTrap Heparin, but was not further purified. The results show that HiTrap Heparin is a suitable column for the binding of both native and recombinant DNA binding proteins directly from bacterial lysates.