Website plays a significant role in success of an e-business. It is the main start point of any organization and corporation for its customers, so it's important to customize and design it according to the visitors' preferences. Also, websites are a place to introduce services of an organization and highlight new service to the visitors and audiences. In this paper, we will use web usage mining techniques, as a new field of research in data mining and knowledge discovery, in an Iranian government website. Using the results, a framework for web content layour is proposed. An agent is designed to dynamically update and improve web links locations and layout. Then, we will explain how it is used to directly enable top managers of the organization to influence on the arrangement of web contents and also to enhance customization of web site navigation due to online users' behaviors. Keywords—Web usage mining, website design, agent, website customization.