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This paper presents the spatial distribution of multiple deprivation in Athens, and links these spatial patterns to the city’s urban development trajectory and the way housing is accessed. Multiple deprivation was measured as the combined concentration of disadvantageous employment situation, access to education and housing conditions. A principal components analysis was utilized for 20 variables from the three said domains. Two components were identified as statistically significant. The analysis covered approximately 3000 urban spatial analysis units (URANU), using data from the population censuses of 1991, 2001 and 2011. The findings unveil that from 1991 to 2011, multiple deprivation in the urban periphery as well as in city center areas worsened. Conditions in many (but not all) working-class areas in the west of Athens, as well as in middle class suburbs in the east, improved or did not get worse. If compared to the urban development trajectory of the city, this distribution means that the historical East–West socio-economic division is getting less pronounced, whereas an important center–periphery dynamic is emerging. The filtering and sorting process of the housing market could explain those trends. It appears that the most affected populations are those outside the Greek family-centered and homeownership-based model of access to housing.