In today’s knowledge based economy knowledge has become the most important competitive advantage of organizations. On the other hand, Information technology improves business values by playing an enabler role in knowledge management infrastructure. Many organizations to take advantage of the benefits of knowledge management systems have introduced, design and use KM systems as a systematic way of applying IT to KM. These systems help organizations to improve competitive power and efficiency in knowledge management. However, there are limitations in reaching these goals leading to failure to make full use of the potential benefits of these systems. Thus, this article studies limitations in these systems through an empirical survey. By reviewing literature, limitation factors divided into three categories: system quality limitations, knowledge quality limitations and service quality limitations. System quality limitations refer to the information processing system criteria. A questionnaire was developed and distributed among the users in several companies that implemented this system. Data were collected and analyzed based on 176 questionnaires related to structural modeling. Then in order to analyze the data, Warp PLS has been employed. The results show that knowledge Quality were statistically and service quality and system quality respectively the most significant factors that affects user dissatisfaction and there is a positive relationship between three limitations redounded to user dissatisfaction of the knowledge management systems.