The Portuguese road network had an extension of 11408 Km in 1998, corresponding to a density of 1.1 Km/Km2. In 1999, a new National Road Plan (PRN2000) was approved, establishing a 16% road network increase over the previous 1985 plan. Several of these new major roads actually cross Natural Parks, Birds Directive and Nature 2000 sites. Habitat loss and fragmentation due to transport infrastructure is clearly a problem in Portugal. Portuguese major road projects are subjected to an Environmental Impact Assessment (EIA) process. The approaches used in the Ecological Impact Assessment (EcIA) of these road projects are mainly focused in small-scaled effects. Research, involving over 40 portuguese road EIAs at different project stages, showed that no consistent ecological criteria was presented to establish the EcIA area of study; further, the methodologies utilized for prediction and evaluation of ecological impacts of transport infrastructures did not translate the effects of habitat fragmentation as they did not address the problems of: • infrastructure as a barrier to the free movement of animals and its implications to population and metapopulation dynamics of the most important species; • infrastructure as a cause of significative edge effect. These are aspects that can impair the EcIA process effectiveness, namely by incorrectly identify the areas for the placement of wildlife crossing structures, planned as part of the mitigation measures associated to the transport infrastructure. The following study presents the application of a methodology (FRAGMet3) that analyses the aspects of habitat fragmentation and deterioration at different scales. This methodology, GIS based, involves: the identification of important natural areas; the delimitation of the area under study; the analysis of potential green corridors and existing linear transport infrastructures; the characterization of the landscape structure for the area directly affected by the infrastructure and for several buffer areas, using soil occupation maps (1:25000). The landscape indices calculated are based in edge, shape, core area and contagion metrics. The analysis can be carried out on three levels, corresponding to three different project stages: corridor selection; alternative selection and project implementation. The results obtained in each stage can be used to establish priorities for field sampling / monitoring in the following phase. We describe the results obtained from the application of FRAGMet3 to the highway IC5 - Mondim / Vila pouca de Aguiar (North Portugal) proposed corridors and alternatives. Fragmentation indices showed clear differences between corredors as well as between alternatives. The practical value of this methodology as a base for decision support in the process of EIA and its following stages analysed.