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Background Healthcare associated infection (HAI) is alarmingly increasing in low income settings. In Tunisia, the burden of HAI is still not well described. We aimed to analyze risk factors independently associated with HAIs in hospitalized patients in Sahloul Hospital for the last five years. Methods We conduct every year a prevalence survey, as part of the program for the prevention and control of HAI at Sahloul Hospital. It is a cross-sectional study of one-day prevalence with a single pathway. All departments were included in the survey, except emergency and hemodialysis services due to their very short length of stay. Data collection was carried out using NosoTun plug (national HAI prevalence survey). Logistic regression was performed to identify independent risk factors of mortality among infected patients with p value less than .05. Results Over five years, prevalence of HAI ranged from 11.4% in 2014 to 7.1% in 2018. In 2014, independent risk factors of HAIs were the use of peripheral venous catheter, central venous catheter, and undergoing a surgery. Intensive care units and surgical departments were independently associated with the occurrence of HAIs. In 2015 and 2016, in addition to the factors already mentioned, antibiotic therapies for the last six months as well as parenteral feeding were also found as independent risk factors. In both 2017 and 2018, intrinsic factors were found in multivariate analysis; in fact diabetes as underlying disease was independently associated with HAIs. Conclusions Identifying risk factors that contribute to develop HAIs may support the implementation of strategies for their prevention, therefore maximizing patient safety. Key messages Identifying risk factors for HAIs may improve patient safety. Insertion of medical devices was the main risk factor for patients over the five years.