Background: The analysis in 2005 of 126 cases wrong site, wrong procedure, wrong patient obtained 76% of wrong site, 11% of wrong procedure and 13% of wrong patients (WHO, 2009). In PKU Muhammadiyah Hospital Unit II has been socialized implementation of site marking operation. However, the implementation of site marking operation there are not in accordance with SOP. This study aimed to evaluate of site marking implementation in the operating room of PKU Muhammadiyah Unit II Yogyakarta Hospital. Method:This study uses a mixed method with sequential explanatory. Total observation sample are 62 respondents and interview sample are 6 respondents. Data obtained using observation, interviews, and documentation. The results of observations taken from the observation checklist and interviewed the informant and then analyzed Results and Discussion: The marking operation is performed based on the type of operation 55% according to the SPO there are 12 general surgery and 22 eye surgery. Implementor, step,and form of site marking are 100% in accordance with the SOP. Place of site marking of are 35.3% accordance with the SOP, the tools that used in site marking are 47% accordance with the SOP. Implementation of site marking to determine the right site, right procedures, and right patient. Obstacles encountered in the implementation of site marking operation that is about logistics, human resources, patient, time and cost, SOP. Recommendations for the implementation of site marking operation that is the socialization of the site marking, creating a effective of the culture, changes SOP, improved logistics, patient education, and one marker for one patient. Conclusion: Marking operations at PKU Muhammadiyah Hospital Unit II overall is already up and running properly in accordance the SOP. Implementation of site marking operation in this study are in accordance with the right site, right procedures and right patient although in practice they found some obstacles. However, some of the recommendations from the Directors in implementation of site marking is expected to make a significant changes for patient safety.