Objective: To analyze the protein expression differences between colonized multidrug-resistant acinetobacter baumannii (MDR-AB) and infectious MDR-AB using comparative proteomics and matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) and to explore the molecular characteristics of MDR-AB infections. Methods: A total of 59 MDR-AB strains including 23 of bloodstream infections MDR-AB and 36 of nasal, pharyngeal or environmental colonization MDR-AB were collected from Beijing Tongren Hospital between January 2008 and December 2011. MALDI-TOF MS cluster analysis was applied to identify the differences of protein expression between infection strains and colonization strains (including patient colonization and environmental colonization) of MDR-AB. Two-dimensional protein differences electrophoresis and MALDI-TOF-TOF MS were used to analyze the protein expression differences between bloodstream infection strain and nasal colonization strain isolated from the same patient. Results: ST92 was the main multiple locus sequence typing of 23 bloodstream infections MDR-AB. Cluster analysis showed that there were differences of protein fingerprint of MADLI-TOF MS between colonized and infectious MDR-AB. Proteomic differences were found between colonization strain and infection strain which were isolated from the same patient. And 9 major different protein spots were identified. They were trigger factor (score of identification was 10 218 and coverage rate was 44%), inosine-5'-monophosphate dehydrogenase (score of identification was 1 919 and coverage rate was 60%), phosphoglycerate kinase (score of identification was 947 and coverage rate was 49%), outer membrane protein 38 (score of identification was 572 and coverage rate was 23%) and so on. Conclusion: There were differences of protein expression between MDR-AB infection strains and colonization strains. And such different proteins could provide experimental evidence for molecular markers research of MDR-AB infections.