Background Nosocomial infection caused by methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) could lead to increased morbidity and mortality. In 2006, VRE nosocomial spread became a reality in our hospital since the first VRE nosocomial infection in 2003. Little is known about the prevalence of coexistence with VRE and MRSA in the patients. The primary objective of the study was to identify the molecular characteristics of epidemic MRSA clones in our hospital and the prevalence of the coexistence with MRSA and VRE in same patients during the 2-year period, 2006-2007.Methods The clinical features, laboratory test results, and therapeutic outcomes of 129 cases who isolated MRSAcollected from January 2006 to December 2007 were retrospectively analyzed. Polymerase chain reaction (PCR) was used to determine mecA-femB type and staphylococcal cassette chromosome mec (SCCmec) type. All the participants were screened for clinical and microbiological data to identify the coexistence of VRE strains with MRSA.Results One hundred and twenty-nine MRSA isolates were included in the study: 71 (55%) from the intensive care unit,35 (27.2%) from the surgical wards and 23 (17.8%) from the medical wards. The most frequent source of isolation of MRSA was sputum (76.7%). From seven patients we isolated MRSA and VRE (E. faecium) simultaneously during their inpatient stay. One hundred and twenty-seven (127/129, 98.4%) MRSA isolates harboured SCCmec type Ⅲ, only 2 MRSA strains contained SCCmec type Ⅱ. All of the 129 MRSA isolates remained sensitive to vancomycin, teicoplanin and linezolid. Higher sensitivity rates were noted for chloramphenicol 99.2% (128/129). Only 20.2% (26/129) of the MRSA isolates were sensitive to rifampin. All isolates presented resistance to multiple antimicrobial agents with high minimum inhibitory concentrations (MICs), including: β-lactams (penicillin, oxacillin, cefoxitin, and cefazolin), tetracycline,erythromycin, gentamicin, and quinolones (ciprofloxacin, levofloxacin, and moxifloxacin).Conclusions The predominant MRSA clone at Beijing Chaoyang Hospital from 2006 to 2007 had the type Ⅲ SCCmec element. All of the MRSA isolates were multiresistant to antimicrobial agents. Emergence of coexistence of MRSA and VRE in the same patient was not rare. Physicians should pay more attention to infections resulting from MRSA and VRE. Aggressive infection control measures should be taken to prevent the transmission of the multidrug resistance organism.