To measure the underregistry of mortality in children under five years old, and the coverage of the Birth Certificate (BC) in municipalities with very low human development index (HDI) in Mexico.We studied all deaths of children under five years old occurred in 2007 and all births occurred in 2007 and 2008 in a sample of 20 municipalities with very low HDI in Mexico. We conducted an intentional search of births and deaths.We identified 12 additional deaths not included in official registries, for an underregistration of 22.6%, and 68.1% of births did not have a BC. Lack of BC was more frequent if the mother did not speak Spanish, if she did not have Seguro Popular if the birth was attended by a traditional midwife. Conclusions. It is necessary to strengthen the registry of deaths and births in municipalities with very low HDI.