Emerging/re-emerging zoonotic diseases are a major global health problem. Linking comprehensive pathogen surveillance of arthropod/vector populations in Uganda with public health surveillance at the regional and international level will make an important contribution to human and animal health in East Africa and the One World One Health concept in general. There will be a focus on rodent-borne pathogens potentially causing disease in humans, wildlife and livestock. A more comprehensive understanding of the ecology of known and unknown rodent-borne zoonotic pathogens is essential for a risk assessment for local and global human and animal health. The establishment of an emerging/re-emerging virus program in Rakai, Uganda is ongoing. The necessary equipment to start investigations into emerging viral disease in the region have been procured and will be transported to Uganda in the following fiscal year. The 2014/2015 Ebola virus outbreak in West Africa has resulted in major delays for planned field expeditions, to set up the lab in Rakai, and to establish contacts with the regional health authorities. Activities are expected to resume shortly.