Abstract： Objective To establish protein fingerprints of common bacteria in clinics and to lay a foundation for rapid identification of bacteria.Methods Strains of Escherichia coli,Klebsiella pneumoniae,Pseudomonas aeruginosa and Staphylococcus aureus were detected by surface enhanced laser desorption and ionization time-of-flight mass spectrometry (SELDI-TOF MS).Stable expression protein peaks were screened and the data was input into the self-constructed Fingerwave software for identification of target bacteria by protein fingerprint comparison.Two hundred and fifty-six clinical isolates,including E.coli,K.pneumoniae,P.aeruginosa and S.aureus were detected and the data was compared with constructed database to evaluate its diagnostic value.Results The protein fingerprints including four common bacteia was used to identify the target bacteria with identification rate of 93.1％ (54/58) for E.coli,87.2％ (75/86) for K.pneumoniae,96.2％ (60/63) for P.aeruginosa and 96.2％ (51/53) for S.aureus,respectively.Conclusion Common bacteria can be rapidly identified by using the protein fingerprint comparison,which provides a powerful tool for bacterial identification.