Southeast Asia is one of the richest reservoirs of biodiversity on earth and home to one of the highest concentrations of endemic species. Many protected areas (PA) have been established across the region, but to date no systematic evaluation of their efficacy has been published because no comprehensive dataset was available which could be fed into an analysis of conservation gaps. We collected the geographic range for 1086 mammal species of Southeast Asia and we built species-specific habitat suitability models for 901 of them. We performed two gap analyses (one based on a combination of distribution models and distribution ranges and one based on distribution ranges only) for each mammalian species, to evaluate the effectiveness of the existing network of PA and to identify priority regions and priority species for expanding and consolidating the network. Our results indicate that 7.5-8.2% of species are not covered by any PA, and 51.6-59.1% are covered only partially. These species are distributed throughout the entire study area and their conservation requires the creation of new PA that can help fill this existing conservation gap. This would be particularly important for species which are endemic of small islands, where species survival is often threatened by the presence of introduced species and habitat conversion. Yet PAs cannot be considered as the ending point of a conservation strategy, because overall, 34% of the species we analyzed (many of which already covered by existing PAs) were at risk of extinction when considering the IUCN red-list criteria. PAs should therefore be considered in a broader framework of all local ecological and socio-economic trends, including the growing human population, growing economy and infrastructure development. © 2008 Elsevier Ltd. All rights reserved.