This paper analyses the potential response of bird species preserved in special protected areas (SPA) of Lithuania to climate change throughout the 21 st century. The effectiveness of SPA territories in recently existing system of their designation and related problems are discussed. The results of analysis show that with withdrawal of the range in north-eastern direction 17 out of the 49 species protected in Lithuanian SPAs and breeding on western, south-western and southern peripheries of entire species range will be primarily affected and are likely to become extinct. The remaining 32 species with recent populations on northern, north-eastern, eastern, north-western peripheries and central part of the species range in Lithuania benefit from climate warming and, most likely, will not get extinct. It is evident that throughout the 21 st century due to climate change 1/3 of the protected species in 72 SPAs designated in Lithuania will be at risk of extinction. A Climatic Atlas of European Breeding Birds (Huntley et al. 2007) predicts extinction of eight more species in the territories of Lithuanian SPA. The model we have applied and our projection, however, fail to confirm this prediction. The analysis of the future prospects for SPA territories in the 21 st century shows all qualifying species to potentially survive in 41 SPA out of the 72 investigated. In four territories up to 1/4 of the qualifying species are likely to become extinct, in 19 territories -from 1/4 to 3/4 and in eight territories all qualifying species are at risk of extinction. Accordingly, slightly over 60% of SPAs in Lithuania will remain functioning in the 21 st century provided that climate change proceeds at the forecasted rate. These changes reveal new urgent practical problems at the science-policy interface. The nature conservation objectives recently formulated on the assumption of climate stability must be replaced by the new working rules adapted to new changing enviromental conditions. We must find a new approach to threats faced by birds and a new vision of their protection, stressing the importance of the knowledge of the species-specific ecology of habitat selection, migratory status of breeding birds, the populations' location within the entire species range as well as trends and scope of the regional climate change for the development of effective measures and ways for bird protection. key words: climate change impact, bird diversity conservation, special protected areas (SPA)