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The authors researched changes in specific habitat types in areas considered to be the most important in Croatia for protection of endangered bird fauna during the period 1990–2000. The analysis focused on four areas in the continental part of Croatia (Danube and Drava River alluvium, Pokupsko depression, Sava River basin, Upper Drava River basin) and four areas in the Mediterranean part (Neretva River estuary, NW part of North Dalmatia, Paško field, Lake Vrana). For the classified habitat types, changes in Corine land cover databases in 1990 and 2000 were analysed. The greatest changes in habitat were detected along the Danube and Drava River alluvium, where more than 8% of the total area changed habitat type, as well along the Sava River basin, where approximately 5% of the total area and the greatest absolute area changed habitat type. The most pronounced changes were detected in forest habitats, where forest degradation prevents the maturation of forest stands. The authors discuss which bird species listed in the Red Data Book of Birds of Croatia may be most impacted by the detected changes in habitat. Special attention was given to a comparison of habitat changes in the Nature Park Lonjsko polje between two raptor species, Aquila pomarina and Haliaeetus albicilla, according to the suitability of habitats where changes occurred.