A clinical decision support system (CDSS) for empirical antibiotic treatment has the potential to increase appropriate antibiotic use. Before using such a system on a broad scale, it needs to be tailored to the users preferred way of working. We have developed a CDSS for empirical antibiotic treatment in hospitalized adult patients. Here we determined in a usability study if the developed CDSS needed changes.Four prespecified patient cases, based on real life clinical scenarios, were evaluated by 8 medical residents in the study. The "think-aloud" method was used, and sessions were recorded and analyzed afterwards. Usability was assessed by 3 evaluators using an augmented classification scheme, which combines the User Action Framework with severity rating of the usability problems and the assessment of the potential impact of these problems on the final task outcomes.In total 51 usability problems were identified, which could be grouped into 29 different categories. Most (n = 17/29) of the usability problems were cosmetic problems or minor problems. Eighteen (out of 29) of the usability categories could have an ordering error as a result. Classification of the problems showed that some of the problems would get a low priority based on their severity rating, but got a high priority for their impact on the task outcome. This effectively provided information to prioritize system redesign efforts.Usability studies improve lay-out and functionality of a CDSS for empirical antibiotic treatment, even after development by a multidisciplinary system.