During the Programming Period 2014–2020, dozens of Greek cities drafted Integrated Territorial Investment programmes, based on Integrated Sustainable Urban Development Strategies (ITI SUDs). The Strategies justified the selection of intervention and activity areas using socio-economic analysis. The parameters of that analysis, as specified by the National Coordination Authority, reflected the socio-economic and functional parameters highlighted in the relevant EU regulations. This paper uses a recently published methodology in order to estimate and map deprivation in Greek cities with over 100,000 inhabitants, and compares the results with the activity areas identified in the ITI SUDs of those cities. The paper also makes an estimation of the potential for micro-segregation in deprived areas, in an effort to uncover the links between deprivation, built form and social composition at the micro-scale. The analysis shows that deprivation is comparatively more pronounced in Athens and Thessaloniki, and that the use of a common methodology to measuring deprivation, but with customized measurement scales, could support a more targeted allocation of urban policy resources. On the other hand, micro-segregation seems to be a factor worth exploring only in Athens and Thessaloniki, and not in Patra, Larissa, Volos and Heraklion, where the building stock in areas of deprivation is mostly low-rise.