Objective: Our aim is to analyze the exoproteins of the epidemic strain and nonepidemic strain of El Tor Vibrio cholerae., Methods: We separated the exoproteins of two El Tor strains, one epidemic strain N16961 and one nonepidemic strain 92-3, by two dimension electrophoresis. All protein spots were identified by MALDI-TOF (Matrix Assisted Laser Desorption Ionization-Time of Flight) mass spectrometry and database referencing., Results: We identified 49 exoproteins from 206 protein spots in epidemic strain and 42 exoproteins from 236 protein spots in nonepidemic strain. Sixty-eight exoproteins were totally identified in two strains, and the proteins with signal peptides were about 55.88% in total. We classified the exoproteins into 10 subgroups according to their functions. Among them were metabolic enzymes, protein maintenance and folding, protein synthesis and signal transduction proteins, which accounted for 36.76% of all the proteins identified. We identified 11 hypothetical proteins and 2 unknown function proteins with signal peptides at the first time, accounting for 19.12%. Transporter, flagellum components, degradation enzymes, outer membrane proteins and toxin accounted for 14.71%, 11.76%, 10.29%, 5.88%, 1.47% separately., Conclusion: We obtained the exoprotein profiles of epidemic strain and nonepidemic strain of El Tor Vibrio cholerae. The reasons of why the flagellum components without signal peptides that are associated closely with virulence could be released out of the bacteria, and why with high hemagglutinin/protease secretion in nonepidemic strains should be analyzed in the future.