Pests and diseases of bananas (Musa spp.) threaten the livelihoods of over 20 million people in the Great Lakes region. Geographic information systems (GIS) provide valuable tools in monitoring, predicting, managing and fighting the spread of pests and diseases. The tools offer opportunities for cost-effective and efficient targeting of control interventions. In monitoring, GIS can be used to determine the spatial extent of a disease, to identify spatial patterns of the disease and to link the disease to auxiliary spatial data. GIS can also be used to predict the projected spread of diseases, to provide input for risk assessment models in pest control and in quantifying changing thresholds of pests and diseases due to climate change. In order to use GIS techniques at a larger scale, a protocol for data collection and management is essential. This paper illustrates the use of GIS tools on data collected to identify critical intervention areas to combat the spread of Banana Xanthomonas wilt (BXW). In a survey covering the Great Lakes region, on-farm incidence of the disease was monitored and precise GPS coordinates of each sampled field were recorded. This enabled accurate mapping of the disease and performing the various spatial analyses, permitting an understanding of the geographical distribution of BXW infection. Data on food security and dependency on banana to rural populations was linked to the BXW severity to target priority areas of interventions and maximize impact.