In this paper, we introduced EXMOTIF, an efficient algorithm to extract structured motifs within one or multiple biological sequences. We showed its application in discovering single/composite regulatory binding sites. In the structured motif template, we assume the gap range between each pair of simple motifs is known. In the future, we plan to solve the motif discovery problem when even the gap ranges are unknown. Another potential direction is to directly extract structured profile (or position weight matrix) patterns.