This study was designed to assess the frequency and risk factors for colonization with MRSA and A. baumanii in the intensive care unit, and to analyse the relationship between colonization and infection with MRSA or A. baumanii. During a 24-day survey period, colonization was studied weekly with nasal, throat and digit skin swabs; nosocomial infections were routinely monitored according to CDC recommendations. Clinical data and invasive procedures were registered during a one-year non-epidemic period; 103 ICU patients hospitalized for more than 7 days were prospectively included. We investigated acquired colonization and nosocomial infection with SAMR or A. baumanii for 87 patients not colonized by SAMR or A. baumanii on admission. The colonization acquisition rate was 56% for MRSA and 27% for A. baumanii. Infection incidence (cases per 1,000 patient-days) was 6.46 for MRSA and 1.61 for A. baumanii. On univariate analysis, acquired MRSA colonization was associated with longer ICU stays, longer mechanical ventilation and longer central venous catheterization. Multivariate analysis only showed an association with longer ICU stay. Acquired A. baumanii colonization was associated with SAPSII, longer mechanical ventilation, and longer central venous catheterization in univariate analysis. Multivariate analysis only showed an association with SAPSII and longer mechanical ventilation. In this study, SAMR or A. baumanii infections were not associated with colonization or clinical setting or invasive procedures.