The settlements show an advanced level of planning
A remote area of the Amazon river basin was once home to densely populated towns, Science journal reports.
The Upper Xingu, in west Brazil, was once thought to be virgin forest, but in fact shows traces of extensive human activity.
Researchers found evidence of a grid-like pattern of settlements connected by road networks and arranged around large central plazas.
There are signs of farming, wetland management, and possibly fish farms.
The settlements are now almost completely overgrown by rainforest.
The ancient urban communities date back to before the first Europeans set foot in the Upper Xingu region of the Brazilian Amazon in the 15th Century.
Professor Mike Heckenberger, from the University of Florida, in Gainesville, said: "These are not cities, but this is urbanism, built around towns."
"They have quite remarkable planning and self-organisation, more so than many classical examples of what people would call urbanism," he said.
Although the remains are almost invisible, they can be identified by members of the Kuikuro tribe, who are thought to be direct descendents of the people who built the towns.
The tell-tale traces included "dark earth" that indicated past human waste dumps or farming, and concentrations of pottery shards and earthworks.
The researchers also made use of satellite images and GPS navigation to uncover and map the settlements over the course of a decade.
The communities consisted of clusters of 60-hectare (150-acre) towns and smaller villages spread out over the rainforest.
Like medieval European and ancient Greek towns, those forming the Amazonian urban landscape were surrounded by large walls. These were composed of earthworks, the remains of which have survived.
Each community had an identical road, always pointing north-east to south-west, which are connected to a central plaza.
In modern settlements, dams are used to funnel fish into weirs
The roads were always oriented this way in keeping with the mid-year summer solstice.
Evidence was found of dams and artificial ponds - thought to have been used for fish farming - as well as open areas and large compost heaps.
The people who once lived in the settlements are thought to have been wiped out by European colonists and the diseases they brought with them.