Today, over half of the world’s population lives in urban areas and it is projected that, by 2050, two out of three people will live in a city. This increased rural–urban migration, coupled with housing poverty, has led to the growth and formation of informal settlements, commonly known as slums. In Mexico, 25% of the urban population now live in informal settlements with varying degrees of deprivation. Although some informal neighbourhoods have contributed to the upward mobility of the inhabitants, the majority still lack basic services. Mexico City and the conurbation around it form a mega city of 21million people that has been growing in a manner qualified as ‘highly unproductive, (that) deepens inequality, raises pollution levels’ (available at: https://www.smartcitiesdive.com/ex/sustainablecitiescollective/making-way-urban-reform-mexico/176466/) and contains the largest slum in the world: Neza-Chalco-Izta. Urban reforms are now aiming to improve the conditions in these slums and therefore it is very important to have reliable tools to measure the changes that are underway. In this paper, we use exploratory factor analysis to define an index of shelter deprivation in Mexico City, namely the Slum Severity Index (SSI), based on the UN-HABITAT’s definition of slum. We apply this novel approach to the Census survey of Mexico and measure the shelter deprivation levels of households from 1990 to 2010. The analysis highlights high variability in housing conditions within Mexico City. We find that the SSI decreased significantly between 1990 and 2000 as a result of several policy reforms but increased between 2000 and 2010. We also show correlations of the SSI with other social factors such as education, health and fertility. We present a validation of the SSI using Grey Level Co-occurrence Matrix (GLCM) features extracted from Very-High Resolution (VHR) remote-sensed satellite images. Finally, we show that the SSI can present a cardinally meaningful assessment of the extent of deprivation compared with a similar index defined by Connolly (Connolly P (2009) Observing the evolution of irregular settlements: Mexico city’s colonias populares, 1990 to 2005. International Development Planning Review 31: 1–35) that studies shelter deprivation in Mexico.