Objective To investigate the changes of protein expression in rat kidney proximal tubular epithelial NRK52E cells during the epithelial to mesenchymal transitions (EMT) process. Methods Comparative proteomics was applied. Proteins extracted from NRK52E cells(three plates treated with TGF-β1 and three plates without treatment) were separated by two-dimensional gel electrophoresis(2-DE). Comparative analysis of 2-DE protein patterns between the two groups were carried out using computerized image analysis. Selected proteins exhibiting significant alternations were identified by mass spectrometry. Western blotting and RT-PCR were performed to examine the expression of the candidated proteins. Results The expression of 22 proteins including transgelin, ARP2/3 complex 21 000 subunit, destrin, ATP synthase α, ubiquitin-conjugating enzyme 9 (Ubc9), and malate dehydrogenase involved in the organization of the cytoskeleton, energy metabolism and post-translational modification were altered during the EMT process. Western blotting and RT-PCR confirmed the differences of several altered proteins, which was consistent with the findings of 2-DE. Conclusion TGF-β1 induces specific changes in the expression of structural, regulatory and metabolic proteins relevant to the complex process of EMT in NRK52E cells. This findings are helpful to understand the molecular mechanism of EMT and expound the chronic progress mechanism of the kidney disease.