Objective: To establish two-dimensional electrophoresis profiles with high resolution and reproducibility from murine brain tissues by human cytomegalovirus(HCMV) infection and paired murine brain tissues and to identify the differential expression proteins. Methods: Forty Kunming mice were randomly divided into infection group (20) injected with HCMVAD169 and control group (20) injected with saline into their brain. After 30 days, the murine brain tissues by HCMV infection and paired murine brain tissues were separated by two-dimensional gel electrophoresis(2-DE),analyzed by Image Master 2D software, and identified by peptide mass fingerprint(PMF) and database searching, and make West blotting analyses the differential expression of individual proteins. Results: Well resolved,reproducible 2-D maps of the above tissues were obtained.Some of the different proteins identified by mass spectrometry(MS) were matched in the SWISS-2D PAGE database, West blotting analyses were further carried out to verify the differential expression of individual proteins. Conclusion: These data will be valuable for studying the diagnosis of disease at an early stage,mechanisms of pathogenic and the key to the development of anti-HCMV medicine.