The Lifeboat and RNAS Culdrose have been called to a boat just off Bishop Rock.
The Lifeboat was launched at 1520 to the singlehanded yaughtsman who was suffering from back and neck injuries.
The RNAS Culdrose helicopter is now at the scene. Scilly is currently experiencing force 7 gales with rough seas.
Falmouth Coastguard are waiting for a report as to whether the man can be air lifted from the boat.