Introduction. Methicillin-resistant Staphylococcus aureus (MRSA) cause nosocomial and community infections. MRSA colonization in hospitals has been described as an important risk factor during hospitalization. Objective. The colonization characteristics of MRSA was described using the tools of molecular biology. Materials and methods. Between February 2007 and February 2008, 705 patients entering a Colombian intensive care unit (ICU) were screened for MRSA by taking nasopharyngeal samples. For 683 of these patients, a weekly follow-up was provided after they left the ICU. The susceptibility of each S. aureus isolate was tested against 11 antibiotics using agar dilution methods. Sixty two percent (62.0%) of the MRSA isolates were characterized at genetic and molecular level with the detection of resistant genes, SCCmec typing using PCR and the genetic profile with pulsed field gel electrophoresis (PFGE). Results. Of the 705 patients screened at entry to the ICU, 182 (25.8%) were colonized by S. aureus, and of these, 51 (7.2%) were MRSA. Of the 683 patients with follow-up, 62 (9.1%) were infected by MRSA contracted in the hospital ICU. The prevalence of the Chilean clone was 76.5% at entry and 88.9% for follow-up patients. Of the 113 patients colonized with MRSA, nosocomial infection was present in 18 patients (16.0%). Three community-acquired MRSA isolates related to the USA300-0114 pandemic clone were identified. These were also positive for Panton-Valentine leucidin cytotoxin genes of S.aureus.