An assessment by more than 200 experts of 1 500 randomly-selected species of snakes, lizards, crocodiles, tortoises and other reptiles, found that 19% were threatened, said the report in the journal Biological Conservation.
Of these, more than a tenth of species were listed as critically endangered, 41% endangered, and nearly half as vulnerable.
The freshwater turtle is particularly at risk, with nearly half of species believed to be close to extinction, said the report compiled by the Zoological Society of London and the International Union for the Conservation of Nature's Species Survival Commission (IUCN).
Among freshwater reptiles as a group, a third was estimated to be close to extinction.
While reptiles like snakes and crocodiles are often reviled by humans, they fulfil a key role in the balance of Nature, both as hunters and prey. Many turtles, for example, are scavengers and clear up decaying flesh, while snakes help control pests like mice.
"Reptiles are often associated with extreme habitats and tough environmental conditions, so it is easy to assume that they will be fine in our changing world," said study author Monika Boehm.
"However, many species are very highly specialised in terms of habitat use and the climate conditions they require for day-to-day functioning. This makes them particularly sensitive to environmental changes."
The report claims to be the first to summarise the global conservation status of reptiles.
"The findings sound alarm bells about the state of these species and the growing threats that they face," said the IUCN's Philip Bowles.
"Tackling the identified threats, which include habitat loss and over-harvesting, are key conservation priorities in order to reverse the declines in these reptiles."
The researchers said reptiles first appeared on Earth about 300 million years ago.