Introduction: Mexico faces important problems concerning income and health inequity. Mexico’s national public agenda prioritizes remedying current inequities between its indigenous and non-indigenous population groups. This study explores the changes in social inequalities among Mexico’s indigenous and non-indigenous populations for the time period 2000 to 2010 using routinely collected poverty, welfare and health indicator data.

Methods: We described changes in socioeconomic indicators (housing condition), poverty (Foster-Greer-Thorbecke and Sen-Shorrocks-Sen indexes), health indicators (childhood stunting and infant mortality) using diverse sources of nationally representative data.

Results: This analysis provides consistent evidence of disparities in the Mexican indigenous population regarding both basic and crucial developmental indicators. Although developmental indicators have improved among the indigenous population, when we compare indigenous and non-indigenous people, the gap in socio-economic and developmental indicators persists.

Conclusions: Despite a decade of efforts to promote public programs, poverty persists and is a particular burden for indigenous populations within Mexican society. In light of the results, it would be advisable to review public policy and to specifically target future policy to the needs of the indigenous population.