PurposeHospital-acquired infection (HAI) is a major safety issue affecting the quality of care of hundreds of millions of patients every year, in both developed and developing countries, including Ethiopia. In Ethiopia, there is no comprehensive research that presents the whole picture of HAIs in hospitals. The objective of this study was to examine the nature and extent of HAIs in Ethiopia.MethodsA repeated cross-sectional study was conducted in two teaching hospitals. All eligible inpatients admitted for at least 48 hours on the day of the survey were included. The survey was conducted in dry and wet seasons of Ethiopia, that is, in March to April and July 2015. Physicians and nurses collected the data according to the Centers for Disease Control and Prevention definition of HAIs. Coded and cleaned data were transferred to SPSS 21 and STATA 13 for analysis. Univariate and multivariable logistic regression analyses were used to examine the prevalence of HAIs and relationship between explanatory and outcome variables.ResultsA total of 908 patients were included in this survey, the median age of the patients was 27 years (interquartile range: 16–40 years). A total of 650 (71.6%) patients received antimicrobials during the survey. There were 135 patients with HAI, with a mean prevalence of 14.9% (95% confidence interval 12.7–17.1). Culture results showed that Klebsiella spp. (22.44%) and Staphylococcus aureus (20.4%) were the most commonly isolated HAI-causing pathogens in these hospitals. The association of patient age and hospital type with the occurrence of HAI was statistically significant.ConclusionIt was observed that the prevalence of HAI was high in the teaching hospitals. Surgical site infections and pneumonia were the most common types of HAIs. Hospital management should give more attention to promoting infection prevention practice for better control of HAIs in teaching hospitals.