Dof proteins are a family of transcription factors that share a unique DNA-binding domain. Dof proteins were found recently in association with diverse promoters of plant-specific genes, suggesting various roles of Dof proteins in plants. Through binding site selection experiments using randomly synthesized DNA, the recognition sequences of four maize Dof proteins were systematically analyzed. All selected oligonucleotides contained an AAAG sequence, suggesting that this sequence is the recognition core of Dof proteins. In fact, a single mutation in this sequence abolished binding of all four Dof proteins. Furthermore, the preference of each Dof protein for the sequence flanking the core motif was also analyzed using oligonucleotides containing a fixed AAAG and random flanking sequences. Similar, as well as distinct, flanking sequences were observed among the optimal binding sites. Changes in the flanking sequences did affect DNA-binding of Dof proteins.