This study aims to explore the effect of the Quality Management Systems (QMS) on the performance of public hospitals. The study has been conducted in the Ministry of Health hospitals with ISO Quality Management System Certificate (n=73) and non-certificated Ministry of Health hospitals (n=73). The performance of hospitals with and without the Quality Management System Certificate was evaluated by eleven performance indicators based on perspective of Balanced Score Card. Performance indicators used in this study were examined separately by 1)hospitals with the QMS and hospitals without QMS, 2)pre-certificated and certificated periods of the hospitals with quality certificate. The comparison of performance indicators of certificated hospitals and non-certificated hospitals pointed to a difference (p<0.05). In addition, significant differences between performance indicators regarding to both pre-certificated and certificated periods of the hospitals (p<0.05) were found.