Objective:To establish Boyden chamber approaches for comparative analysis of the cell body and pseudopodium protein or RNA of chemotactic breast cancer cells. Methods:Under EGF stimulation,the cell body and pseudopodium protein or RNA of MDA-MB-231 breast cancer cells were separated using Boyden chamber approaches. Then the differential expression of Rab gene family in cell bodies and pseudopodia of MDA-MB-231 breast cancer cells were analyzed. Results:Protein or RNA of cell bodies and pseudopodia were successfully separated and used to analyze the differential expression of Rab gene family in MDA-MB-231 breast cancer cells. We found that 21 Rab genes were highly expressed in cell bodies,16 Rab genes were highly expressed in pseudopodia,and the other 24 Rab genes were equally expressed in cell bodies and pseudopodia. Conclusion:These results make advances in our understanding of the molecules that abundantly located in breast cancer cells pseudopodia.