Background: To characterize and compare the epidemiological and microbiological aspects of community and healthcare-associated mrsa (CA-mrsa, and HA-mrsa) cases in Iran, this prospective cohort study was conducted from January to December 2008 in seven hospitals.Patients and methods: Staphylococci were isolated from 109 hospitalized patients. mrsa isolates were classified into HA-mrsa and CA-mrsa based on clinical features.Antibacterial susceptibility patterns of the isolates to eight antibiotics routinely used to treat infected patients were determined according to standard agar dilution methods.Staphylococcal Cassette Chromosome mec (SCCmec) type of isolates and their correlation with antimicrobial susceptibility patterns in CA and HC isolates were determined.Results: Of 109 isolates, 15 (13.7%) were community-associated and 94 (86.3%) were healthcare-associated mrsa.The most frequent SCCmec types in the studied hospitals were SCC mec type I (56.9%) and type II (22%). Relatively high resistance (>60%) of the mrsa to the seven tested antibiotics including: ciprofloxacin, trimethoprimsulfamethoxazole, clindamycin, rifampin, erythromycin, tetracycline and doxycycline were noticed.Conclusion: To our knowledge, this is the first time that the analysis of SCCmec type is carried out in Iran according to the clinical criteria. Difference in the prevalence of HC-mrsa and CA-mrsa based on the clinical and epidemiological features may indicate the need for revisiting the classification of mrsa. The high prevalence of multidrug resistant mrsa could be as a result of the excessive use of antibiotics in the hospitals. Therefore, periodical assessment of antibacterial susceptibility patterns of the mrsa strains is warranted.