Quox-1 is the only gene in the hox family whose expression occurs throughout the development of the central nervous system. Using the Quox-1 homeodomain produced in a bacterial expression system, we were able to identify DNA-binding targets of the Quox-1 protein from a library of randomly generated oligonucleotides by the selection and amplification binding (SAAB) technique. The results indicated that the Quox-1 protein recognizes a new consensus sequence, 5'-CAATC-3', which has not been reported for any other Hox family homeoprotein. In addition, electromobility shift assay further confirmed that the Quox-1 homeoprotein preferentially binds to the 5'-CAATC-3' sequence, but not to the binding sites for other Hox class homeoprotein (TAAT) or NKX class homeoprotein (CAAG). Based on mutation analyses of the DNA sequences, we found that the 5'-CAATC-3' core sequences are required for high affinity binding by the Quox-1 protein. Furthermore, mutation analyses of the Quox-1 homeodomain showed that one of the major determinants participating in recognition of a minor groove is the Gln6 and Thr7 in the N-terminal arm of the homeodomain.