Jean-Pierre Sauvage, Sir Fraser Stoddart and Bernard Feringa will share the 8m kronor (£727,000) prize for the design and synthesis of machines on a molecular scale.
They were named at a press conference in Sweden.
The machines conceived by today's laureates are a thousand times thinner than a strand of hair.
They could slip inside the human body to deliver drugs from within - for instance, applying pharmaceuticals directly to cancer cells.
This field of nanotechnology could also yield applications in the design of smart materials.