Skyward Sword takes place before Ocarina of Time

In an interview with the Official Nintendo Magazine, Eiji Aonuma confirmed that Skyward Sword is set to take place before Ocarina of Time. Aonuma said, "yes, there is a master timeline but it is a confidential document! The only people to have access to that document are myself, Mr. Miyamoto and the director of the title. We cant share it with anyone else!"

Zelda timeline debates are never ending, being a source of fierce debate amongst many Zelda fans. But with the creation of the Master Sword being explained in Skyward Sword, it makes sense that it should take place before Ocarina of Time.

Source: Official Nintendo Magazine