A major initiative in Europe is the protection of its biodiversity. To accomplish this, specific areas from all countries of the European Union are protected by the establishment of the "Natura 2000" network. One of the major threats to these areas and in general to ecosystems is soil erosion. The objective of this study was to quantitatively estimate surface soil losses for three of these protected areas that are located on semi-arid islands of the Mediterranean. One Natura 2000 area was selected from each of the following islands: Sicily in Italy, Cyprus and Rhodes in Greece. To estimate soil losses, Gerlach troughs were used. These troughs were established on slopes that ranged from 35-40% in four different vegetation types: i) Quercus ilex and Quercus rotundifolia forests, ii) Pinus brutia forests, iii) "Phrygana" shrublands and iv) vineyards. The shrublands had the highest soil losses (270 kg ha(-1) yr(-1)) that were 5-13 times more than the other three vegetation types. Soil losses in these shrublands should be considered a major concern. However, the other vegetation types also had high soil losses (21-50 kg ha(-1) yr(-1)). Conclusively, in order to enhance and conserve the biodiversity of these Natura 2000 areas protective management measures should be taken into consideration to decrease soil losses.