On the basis of the crystal structure of the trp repressor/operator complex, it has been proposed that the specificity of the interaction can be explained not only by direct hydrogen bonding and non-polar contacts between the protein and the bases of its target DNA, but also by indirect structural effects and water-mediated interactions. To understand the contribution of DNA structure and hydration in this context, the structure of the free DNA must be compared with its structure when complexed with the protein. Here we present the high-resolution crystal structure of the trp operator region that is most important in the recognition process. By comparing the free and bound states of the DNA regulatory sequence, we show that the structure and hydration of the DNA target are important elements in its recognition by the repressor protein.