Nowadays most organizations have found that improving the quality of goods and services is the necessary condition to attend and survive in the market and in universal competition. ISO quality management system encompasses requirements for creating, deploying, implementing and maintaining quality management system. The purpose of this research is to investigate the effectiveness of implementing quality management system in some ministry of energy’s subsidiaries in Isfahan province to whom the ISO certificate is given. In order to do that, the research questionnaire was made and data was collected from statistical society containing managers of subsidiaries. The results show that in the above mentioned subsidiaries, after receiving ISO certificate, the desired goals of the quality management system has not been fulfilled generally. The results indicate that lack of knowledge about the capabilities of human resources in implementing the quality management system and lack of efficient staff, lack of continuous control and supervision, exclusiveness of the services and lack of competing conditions, lack of trust among senior managers about the usefulness of quality management system and also lack of sufficient support and relying on dissatisfactory old processes has paved the way for inefficiency of quality management system.