Objective To investigate the effect of position of hexahistine in recombinant protein on nickel chelating affinity chromatography. Methods Target genes were amplified by PCR, then cloned into pMD18-T and sequenced. Two recombinant expression plasmids-pET28-His-CpnlO-IL-4 and pET28-CpnlO-His-IL-4 were constructed to express two kinds of proteins which have hexahistine (6-His tag) in different positions in E. coli BL21 (DE3 ) respectively. Expression products were identified by SDS-PAGE and Western-blot and purified by Ni2+ affinity chromatography. Results Two kinds of fusion proteins could be combined with anti-histine single cloned antibody. Fusion protein His-Cpn10-IL-4 could be separated and purified by nickel chelating affinity chromatography , while fusion protein His-Cpn10-IL-4 could not be purified by this technique. Conclusion When fusion protein is purified by Ni2+ affinity chromatography, the position of 6-His tag is very important for the purification of fusion protein. 6-His tag could be placed at the amino terminal and carboxy terminal of fusion protein except the middle.