Understanding the complex spatio-temporal relationships between environmental pollution and disease and identifying exposures to environmental hazards in high-risk populations are essential elements of an effective environmental and public health management program. Modern computer technologies, such as geographic information systems (GIS), provide cost-effective tools for evaluating interventions and policies potentially affecting health outcomes. GIS analysis or display of environmental health data is also helpful in explaining disease patterns in terms of relationships with social, institutional, technological, and natural environments. This paper examines major issues related to the application of GIS in environmental health sciences. Specifically, the paper presents and discusses the basic principles, potential benefits, and major limitations of GIS in environmental health research. A real-world example application involving development and implementation of a prototype system called EMPHASIS (EnvironMental and Public Health datA analySIs System) to facilitate management, analysis, display, and presentation of environmental, socio-demographic, and health outcome data in Iowa is described. From the discussions and the example application, it is concluded that GIS can significantly add value to environmental and public health data in areas such as exploratory data analysis, hypotheses generation, confirmatory data analysis, and decision-making. The widespread adoption of GIS in these areas, however, is impeded by issues such as inconsistent spatial scales of the data, data quality and currency, lack of appropriate statistical functions for data analysis and interpretation, and data security and confidentiality.