Rice transcription factor IDEF1 specifically binds the iron deficiency-responsive cis-acting element IDE1. IDEF1 belongs to an uncharacterized branch of the plant-specific transcription factor family ABI3/VP1 and exhibits the sequence recognition property of efficiently binding to the GATGC sequence of IDE1. IDEF1 are constitutively present in rice roots and leaves. IDEF1-GFP fusion localized to the nucleus. Transgenic studies show IDEF1 transactivates IDE1-mediated expression only in iron-deficient roots; Induced IDEF1 exhibit substantial tolerance to iron deficiency in both hydroponic culture and calcareous soil. Overexpression of IDEF1 enhances expression of the ion deficiency-induced transcription factor gene OsIRO2.