Malaria is a mosquito-borne disease of global concern with 1.5 to 2.7 million people dying each year and many more suffering from it. In Indonesia, malaria is a major public health issue with around six million clinical cases and 700 deaths each year. Malaria is most prevalent in the developing countries of the world. Aid agencies have provided financial and technical assistance to malaria-prone countries in an effort to battle the disease. Over the past decade, the focus of some of this assistance has been in the provision of geographic information systems (GIS) hardware, software and training. In theory, GIS can be a very effective tool in combating malaria, however, in practice there have been a host of challenges to its successful use. This review is based, in part, on the literature but also on our experience working with the Indonesian Ministry of Health. The review identifies three broad problem areas. The first of these relates to data concerns. Without adequate data, GIS is not very useful. Specific problem areas include: accurate data on the disease and how it is reported; basic environmental data on vegetation, land uses, topography, rainfall, etc.; and demographic data on the movement of people. The second problem area involves technology - specifically computer hardware, GIS software and training. The third problem area concerns methods - assuming the previous data and technological problems have been resolved - how can GIS be used to improve our understanding of malaria? One of the main methodological tools is spatial statistical analysis, however, this is a newly developing field, is not easy to understand and suffers from the fact that there is no agreement on standard methods of analysis. The paper concludes with a discussion of strategies that can be used to overcome some of these problems. One of these strategies involves using ArcView GIS software in combination with ArcExplorer (a public domain program that can read ArcView files) to deal with the problem of needing multiple copies of GIS software. Another strategy involves the development of a self-paced training package that can be used to train individuals