According to the Joint Monitoring Program of the World Health Organization and UNICEF, three quarters of the Beninese population had access to an improved water source in 2008, whereas 12% had access to improved sanitation. The share rose from 63% concerning water and from 5% concerning sanitation in 1990. Coverage in urban areas is considerably higher than in rural areas.
Wastewater treatment is extremely rare in Benin. In most cases, wastewater is not disposed appropriately. According to a 2001 national health survey, in the cities of Cotonou, Parakou and Porto-Novo, two out of 1,000 households dispose their wastewater in a correct way, while most of them discharge it directly into the nature or drains. This leads to pollution and can cause water-borne diseases like malaria and typhoid fever.
The 2014 CIA estimated average life expectancy in Benin was 61.07 years.
About 16% of married women (age 15 to 49) used contraception in 2000. The total fertility rate was 6.4 per woman in 1999.
Yellow fever has all but disappeared. Meningitis, once endemic in the north, now appears only sporadically.
Yaws has been almost totally eradicated in the northern part of the country. Sleeping sickness (trypanosomiasis) has also been greatly reduced in the north. In 2002, 203 new cases of cholera were reported.
The HIV/AIDS in Benin prevalence was 1.90 per 100 adults in 2003. As of 2004, there were approximately 68,000 people living with HIV/AIDS in the country. There were an estimated 5,800 deaths from AIDS in 2003.
In 2002, malnutrition was prevalent in an estimated 25% of children under five years old.
In June 2011, the United Nations Population Fund released a report on The State of the World's Midwifery. It contained new data on the midwifery workforce and policies relating to newborn and maternal mortality for 58 countries. The 2011 maternal mortality rate per 100,000 births for Benin is 410. This is compared with 468.9 in 2008 and 587.6 in 1990.
The under 5 mortality rate, per 1,000 births is 121 and the neonatal mortality as a percentage of under 5's mortality is 27. The aim of this report is to highlight ways in which the Millennium Development Goals can be achieved, particularly Goal 4 – Reduce child mortality and Goal 5 – improve maternal death. In Benin the number of midwives per 1,000 live births is 4 and the lifetime risk of death for pregnant women is 1 in 43.
According to a 2013 UNICEF report, 13% of women had undergone female genital mutilation.