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Background: Colonization is an important risk factor for consecutive infection, but little is known about incidence and initial pattern on admission to respiratory intensive care units (RICU). Objective: To study the bacterial colonization during the first 24 h after admission to a RICU. Methods: Endotracheal aspirates, gastric juice, and pharyngeal and rectal swabs of 55 consecutive patients were cultured (45 men, age 66 ± 14 years, APACHE II 20.1 ± 5.6, no parenchymal infection). All samples were taken within the first 24 h after admission to a RICU. Potentially pathogenic microorganisms were grouped as community (c-PPM) and hospital acquired (h-PPM), and risk factors for colonization of each body site as well as for overall colonization (all sites excluding rectum) were identified by logistic regression analysis. Results: The trachea was colonized in 18% of the intubated patients with c-PPMs and in 11% with h-PPMs. Candida spp. were the most frequent c-PPMs isolated from trachea, pharynx, and stomach (excluding rectal swabs), and Pseudomonas aeruginosa was the most frequently isolated h-PPM in trachea. The incidence of overall colonization was 49% for c-PPMs (predominantly Escherichia coli) and 18% for h-PPMs (predominantly P. aeruginosa). Admission to the hospital ≧48 h before ICU admission was an independent risk factor of colonization with h-PPMs in univariate (33 vs. 7%, p = 0.015) and multivariate analyses (odds ratio 7.2, 95% CI 1.4–38.3; p = 0.0197). Conclusions: Colonization of the trachea with c-PPMs was already present in every 5th and with h-PPMs in every 10th intubated patient during the first 24 h of RICU admission even in the absence of parenchymal infections. Hospitalization more than 48 h prior to RICU admission was a risk factor of colonization with h-PPMs.