IDEF2 is a novel NAC transcription factor in rice, it recognizes the iron deficiency-responsive element 2 (IDE2), predominantly CA(A/C)G(T/C)(T/C/A)(T/C/A) motif. IDEF2 transcripts are constitutively present in rice roots and leaves. IDEF2:GFP shows expression localized to the nucleus. RNAi and CRES-T analysis showed repression of IDEF2 caused aberrant iron homeostasis in rice and also down-regulated other iron-deficiency related genes, such as OsYSL2. IDEF2 bound to OsYSL2 promoter region containing the binding core site, suggesting the direct regulation of OsYSL2.