Despite substantial conservation efforts, biodiversity continues to decline and further conservation action is needed. This imposes significant opportunity cost on local communities, particularly in developing countries where livelihood depends strictly on land use and agricultural activities. Incorporating socio-economic data into methods for the identification of conservation priorities can reduce conflicts between socio-economic development and biodiversity conservation. We present a systematic selection of priority sites for the conservation of 353 Ugandan mammals and amphibians. We used the suitable habitat as an estimate of the area potentially occupied by each species inside its geographic range, and estimated the opportunity cost based on data on agricultural profit. We used the software Marxan to identify the sites that need to be added to the existing protected areas (IUCN categories I-IV) to conserve Ugandan mammals and amphibians at a minimum cost. In addition to the existing protected areas, covering ca. 17,100 km2, ca. 57,500 km2 of land should be protected to achieve the conservation target for amphibians and mammals, bringing the coverage to ca. 38% of the country. The sites that are irreplaceable for the target achievement occupy ca. 32,800 km2, are mostly located in the Western and Eastern regions and overlap with the Eastern Afromontane hotspot and the Albertine Rift. The yearly agricultural profit from these sites amounts to ca. 540,700,000 US$, or 16,524 US$/km2 (2008 value).