Indonesia is one of the countries in Southeast Asia where malaria is a prominent public health concern with an estimated 15 million malaria cases annually and 42,000 deaths. The study explores the environmental risk factors of malaria guided by an eco epidemiological model of malaria transmission. A longitudinal and cross sectional approach has been employed for data gathering of the environmental variables, spatial and temporal patterns of malaria transmission, malaria vectors behaviour and human risk factors of malaria transmission in Indonesia. Three different regions in Indonesia were used for the study. The first area is West Timor which has the highest malaria incidence in Indonesia. The second location is Sukabumi District of West Java, which had a malaria outbreak in 2003. The final location is Kebumen District of Central Java, which has one of the highest malaria pocket areas in Java. All areas were divided into three different topographical settings - coastal, hilly and highland areas. In each study areas, the environmental data were analysed using t-test, ANOVA, Pearson Correlation, and General Linear Model Repeated Measures. Further, LISA (Local Indicators of Spatial Association) analysis using GIS was employed to explore local malaria spatial distribution and generate malaria maps for the malaria transmission areas based on the local spatial association. Adult mosquito (Anopheles spp) surveys were used to explore malaria vectors behaviour in different areas and different topographical settings. Finally, an interview program was used to collect data in order to understand human risk factors in malaria transmission. [...]