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This study aimed to examine the characteristics of HCWs infected with COVID-19 and factors associated with healthcare-associated infection. A cross-sectional study, using secondary data of COVID-19 HCW cases from a registry developed by the Occupational and Environmental Health Unit (OEHU) in Kedah State Health Department, Malaysia, was analysed using Excel and STATA version 14.0. Descriptive analysis and multiple logistic regression were conducted to identify the factors for healthcare-associated COVID-19 infection. A total of 1679 HCWs tested positive for COVID-19 between 1 January 2021 and 19 September 2021. The infection was mainly non-healthcare-associated (67.0%), with healthcare-associated cases contributing to only 33% of the cases. The significant factors associated with healthcare-associated transmission were the following: doctor (aOR = 1.433; 95% CI = 1.044, 1.968), hospital setting (aOR = 1.439; 95% CI = 1.080, 1.917), asymptomatic (aOR = 1.848; 95% CI = 1.604, 2.130), incompletely or not vaccinated (aOR = 1.400; 95% CI = 1.050, 1.866) and CT-value ≥ 30 (aOR = 2.494; 95% CI = 1.927, 3.226). Identifying factors of healthcare-associated infection would help in planning control measures preventing healthcare-associated transmission in the workplace. However, more than half of COVID-19 cases among HCWs involved non-healthcare-associated COVID-19 infection, and, thus, requires further study to identify high-risk behaviours.