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In recent years infectious disease occurs frequently around the world especial in the Mekong river sub region. Spatial information plays a very important role in these disease emergency responses. In order to control and monitor the disease's spread, a public health and disease control web geographic information system is built in the China Next Generation Internet (CNGI) environment. The system is used for the sharing of public health and disease control information in this regional. The system is consisted of CNGI hardware and a WebGIS software system. CNGI hardware contains the IPV6 gateways and switches. The WebGIS consisted of service and client. The service side includes the database, the WebGIS web service and a web portal. The client only needs a web browser. The database includes five parts which is the basic geographic data, the sanitation data, the statistics of the disease, the epidemic disease source data and the outbreak epidemic data. We designed three main functions including the public health and disease information browsing, the epidemic reporting and the emergency commanding. We can view the disease distribution on the map. In one word, CNGI provided a fast band width, multi-IP addressed, QoS and safety environment. The web based public health and disease control GIS system in Mekong is a good example to show how to gathering data, analysis and visualization.