Hepatocyte growth factor (HGF) and its specific receptor MET play a role in many physiological functions including proliferation, migration and morphogenesis. Recently, research results in our laboratory showed that recombinant HGF variants (NK1, NK2, NK3 and NK4) became antagonists to HGF/MET pathway by suppressing proliferation, migration and invasion in human breast cancer cells (MDA-MB-435S, MDA). Similar results were achieved when HGF variants genes were introduced in MDA cells. To understand the molecular mechanism of breast cancer cells metastasis suppressed by HGF variants, MDA and five transfectants, including MDA-GFP, MDA-NK1, MDA-NK2, MDA-NK3 and MDA-NK4 cells were used for proteomic analysis using two-dimensional electrophoresis (2-DE). Differential analysis revealed that a total of 56 polypeptides were differentially expressed through five sets of comparison using wild-type MDA cells as a control. A total of 17 polypeptides were shown differential expression between MDA and MDA-GFP cells, with 11 down-regulated and 6 up-regulated. Eighteen polypeptides were differentially expressed between MDA and MDA-NK1 cells, with 15 down-regulated and 3 up-regulated. There were 22 differentially expressed polypeptides found between MDA and MDA-NK2 cells, in which 14 were down-regulated and 8 were up-regulated. Sixteen polypeptides were shown differentially expressed between MDA and MDA-NK3 cells, with 11 down-regulated and 5 up-regulated. A total of 18 polypeptides were shown differential expression between MDA and MDA-NK4 cells, with 15 down-regulated and 3 up-regulated. Proteomic analysis showed that a total of 43 polypeptides were differentially expressed through four sets of comparison (MDA-GFP and MDA-NK1, MDA-GFP and MDA-NK2, MDA-GFP and MDA-NK3, and MDA-GFP and MDA-NK4). To understand the differential expression among different HGF variants-transfected MDA cells, three sets of cross analysis were also carried out (MDA-NK1 and MDA-NK2, MDA-NK1 and MDA-NK3, and MDA-NK1 and MDA-NK4) and the results showed that a total of 37 differentially expressed polypeptides were found in the three sets of comparison. Similarly, when MDA-NK2 cells were used as a control to compare with MDA-NK3 and MDA-NK4 cells, 34 significantly differential expressed polypeptides were found. The last set of comparison between MDA-NK3 and MDA-NK4 cells, 19 polypeptides were found significantly differential expression. Therefore, our current results revealed that the differentially expressed polypeptides in MDA-MB-435S cells and HGF variants-transfected MDA cells could be related to the inhibition of proliferation and migration of human breast cancer cells by HGF variants.