The development of Latin American cities is characterized by formal and informal urban development patterns, weak land-use planning, inequitable economic opportunities, and unequal social divisions. These and other factors have created divergent, and highly fragmented patterns of spatial segregation at all geographic levels. However, little empirical evidence has captured the extent and magnitude of spatial segregation of the poor within specific mega-cities. The combination of advanced spatial segregation indicators with statistical measures allows for the detection and measurement of segregation between multiple groups at multiple scales across the urban region. The paper explores the extent of spatial segregation of different socio-economic groups in Lima, Peru, using 1993 census and more recently released data, presenting a methodology for integrating older and newer data sources. The results indicate that segregation across the Metropolitan Region is localized, with “pockets” of difference across otherwise seemingly homogeneous areas.