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Background: Healthcare-associated infections (HAIs) cause increases in length of stay, mortality, and healthcare costs. A previous study conducted in Taiwan obtained similar results to those reported in Korea and Japan in 2015. Changes in microorganisms have been noted in recent years. Understanding the recent condition of HAIs in intensive care units (ICUs) can enable healthcare providers to develop effective infection control protocols to reduce HAIs. Methods: We used the Taiwan Nosocomial Infection Surveillance System to evaluate the incidence densities of HAIs, the proportions of causative pathogens, and the proportions of antimicrobial resistance (AMR). The Poisson regression model was constructed to incidence density, and the chi-square test was used to assess proportion. Results: The incidence density of HAIs decreased 5.7 to 5.4 per 1000 person-days. However, the proportions of Klebsiella pneumoniae and Enterococcus faecium significantly increased. In addition, the proportions of carbapenem-resistant K. pneumoniae and vancomycin-resistant Enterococcus faecium significantly increased over time. Conclusion: Analysis of the microorganisms involved in HAIs in ICUs showed elevated proportions of K. pneumoniae and E. faecium with AMR. Infection control protocols have been implemented for several years and require improvements regarding environmental cleanliness and medical staff prevention.