During the twenty years since Obasanjo had left power in 1979, some 75 million Nigerians had been born and 25 million had died. Total population numbers were contentious but may have increased between 1979 and 1999 from about 70 million to 120 million. A continuing high birthrate more than compensated for child mortality 60% higher than the average in low-income countries. When Obasanjo took office in 1999, half of all Nigerians were no more than seventeen years old. The problems facing the regime can be understood only against this demographic background.

A major reason for high mortality was deplorable public health services, which the World Health Organisation ranked 187th among its 191 member states in 2000–1. During the 1990s public health expenditure had absorbed about 0.2% of GDP, the lowest proportion in the world, equalled only by Myanmar. In 1998 only an estimated 35% of the population had access to modern health services, some 80% of which were located in the South. The proportion of children aged 12–23 months who were fully immunised fell between 1990 and 1999 from 30 to 17%. In the latter year, 46% of children were judged to be malnourished. Obasanjo's regime more than doubled the proportion of federal expenditure allocated to health and launched a new primary health care campaign, appropriating local government funds with the aim of building a clinic in each of the 774 local government areas.