Background: The expansion of urban slums is a key challenge for public and social policy in the 21st century. The heterogeneous and dynamic nature of slum communities limits the use of rigid slum definitions. A systematic and flexible approach to characterize, delineate and model urban slum structure at an operational resolution is essential to plan, deploy, and monitor interventions at the local and national level.Methods: We modeled the multi-dimensional structure of urban slums in the city of Salvador, a city of 3 million inhabitants in Brazil, by integrating census-derived socioeconomic variables and remotely-sensed land cover variables. We assessed the correlation between the two sets of variables using canonical correlation analysis, identified land cover proxies for the socioeconomic variables, and produced an integrated map of deprivation in Salvador at 30 m × 30 m resolution.Results: The canonical analysis identified three significant ordination axes that described the structure of Salvador census tracts according to land cover and socioeconomic features. The first canonical axis captured a gradient from crowded, low-income communities with corrugated roof housing to higher-income communities. The second canonical axis discriminated among socioeconomic variables characterizing the most marginalized census tracts, those without access to sanitation or piped water. The third canonical axis accounted for the least amount of variation, but discriminated between high-income areas with white-painted or tiled roofs from lower-income areas.Conclusions: Our approach captures the socioeconomic and land cover heterogeneity within and between slum settlements and identifies the most marginalized communities in a large, complex urban setting. These findings indicate that changes in the canonical scores for slum areas can be used to track their evolution and to monitor the impact of development programs such as slum upgrading. © 2013 Hacker et al.; licensee BioMed Central Ltd.