Objective To study the different expressions of proteins in different regions of cerebellum. Methods Proteins isolated from the anterior lobe, the posterior lobe and the paraflocculus of cerebellum were separated by twodimensional (2D) gel electrophoresis. Using PDQuest software, proteins on the 2D maps were selected and further analyzed by matrixassisted laser desorption /ionization twostage time of flight (MALDI TOF/TOF) tandem mass spectrometry. The mass spectrometric data were used to identify the proteins through the general proteomics standard (GPS) search and Mascot database. Results There were five proteins identified in three regions of cerebella. The level of pyruvate kinase isozyme M2 was higher in the anterior and posterior lobes of cerebellum than in the paraflocculus. Heterogeneous nuclear ribonucleoprotein L and eukaryotic translation elongation factor 2 were only identified in the posterior lobe with low expression, and were not detected in other regions. The expressed sequence AI429145 was only detected in the posterior lobe. The paraflocculus expressed higher level of ATPase (H+ transporting, VO subunit D, isoform 1) compared with the anterior and posterior lobes.Conclusion The different expressions of those proteins may be important for the understanding of the specific functions