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All three species of Orangutan are critically endangered according to the IUCN Red List of mammals. They are legally protected from capture, harm or killing in both Malaysia and Indonesia, and are listed under Appendix I by CITES, which prohibits their unlicensed trade under international law. The Bornean orangutan range has become patchy, being largely extirpated from several parts of the island, including the southeast.

The largest remaining population is found in the forest around the Sabangau River, but this environment is at risk. The Sumatran orangutan is found only in the northern part of Sumatra, most of the population inhabiting the Leuser Ecosystem. The Tapanuli orangutan is found only in the Batang Toru forest of Sumatra.

Birute Galdikas wrote that orangutans were already endangered by poaching and deforestation when she began studying them in 1971. During the early 2000s, orangutan habitats decreased rapidly because of logging and forest fires, and fragmentation by roads. A major factor has been the conversion of vast areas of tropical forest to palm oil plantations in response to international demand. Hunting is also a major problem, as is the illegal pet trade. Orangutans may be killed for the bushmeat trade and bones are secretly traded in souvenir shops in several cities in Indonesian Borneo. Conflicts between locals and orangutans also pose a threat. Orangutans that have lost their homes often raid agricultural areas and end up being killed by villagers. Locals may also be motivated to kill orangutans for food or because of fear and self-defense. Mother orangutans are killed so their infants can be sold as pets, and many of these infants die without the help of their mother. Since 2012, the Indonesian authorities, with the aid of the Orangutan Information Center, confiscated 114 orangutans, 39 of which were pets.

Estimates between 2000 and 2003 found 7,300 Sumatran orangutans and between 45,000 and 69,000 Bornean orangutans remain in the wild. A 2016 study estimates a population of 14,613 Sumatran orangutans in the wild, doubling previous population estimates.Fewer than 800 Tapanuli orangutan are estimated to still exist, which puts the species among the most endangered of the great apes.