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 emerging/re-emerging virus programs in Rakai, Uganda (ICER site) and the campus of the Uganda Virus Research Institute (UVRI), Entebbe, 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. We have started the process of developing and establishing molecular and serological detection assays for several pathogens including arenaviruses, bunyaviruses, coronaviruses filoviruses, and flaviviruses. Some of these assays are ready to be moved into the ICER site in Uganda. The 2014/2016 Ebola virus outbreak in West Africa, the continuing MERS-coronavirus cases in the middle East, the ongoing Lassa fever outbreak in Nigeria, and the response to Zika virus have resulted in major delays for planned field expeditions, to set up the laboratories, and to establish contacts with the regional health authorities. Activities are expected to resume shortly.