Territorial impact assessment (TIA) aims at informing policy-makers on the policy impacts on different geographical areas (‘territorial units’). This paper presents a methodology for TIA which was tested on four European Union (EU) directives and their likely impacts on territorial units in Slovenia. This involved clustering Slovenian statistical (NUTS 3) regions according to their policy-relevant characteristics. The evaluation framework was reflecting the specific territorial cohesion objectives at corresponding governance levels (EU, national, local). This exercise indicates that there are some significant differences among Slovenian regions for different impacts, which become somewhat blurred when aggregated. Furthermore, the meaning of impacts differs depending on the governance level from which they are viewed. We conclude that important differences may be lost when impacts are generalized in policy assessments.