Through first-principles pseudopotential total-energy calculations, we investigate the formation energetics and the electronic structures and structural properties of the native defects available in LiNbO3. We found that the formation enthalpies of Li-vacancy and Nb-antisite defects where lower compared to other defects. We examined the detailed electronic structures and structural properties of Nb-antisite. We identified a large Jahn-Teller distortion of Nb-antisite that can be induced by light illumination, by which the electronic structure is also remarkably changed. We discuss the role of the bistability of Nb-antisite in the photorefractivity.