The theory has been developed following the case of one Swiss woman who, despite being born with no forearms or legs, was able to feel the sensation of moving them.
Nearly all amputees have some feeling of "phantom limbs", meaning they experience some feeling as if they were still there.
Experts think this is because the brain cells once involved in sensing them are still sending signals.
However, when people born without limbs have claimed this, they have been dismissed as wishful thinkers.
It was thought that if the limbs never existed, the developing brain would never lay down the brain cells needed to feel or control them.
However, reports New Scientist magazine, experiments on a 44-year-old woman were able to disprove this.
Stimulated
Dr Peter Brugger, and colleagues from the University of Zurich Hospital, magnetically stimulated parts of the brain that normally sense limb movement.
The woman reported feeling as if her limbs were moving - and scans revealed that there was indeed activity in parts of the brain normally associated with preparing and visualising movement - although not in the part which actually controls it.
Dr Brugger said: "What really shows that our subject's phantom hands and feet are not mere products of wishful thinking is a cognitive test."
Another expert on phantom limbs, Dr Vilayanur Ramachandran from the University of California in San Diego, said he felt it showed that the development of the brain was more specified in more detail by genetics than previously thought.
He said: "So even though the "hand" area gets input from an arm stump, when it fires, you feel a hand, even if you never had one."