Motifs are essential sites and therefor usually conserved in proteins. Motifs play a crucial role not only in protein world but also in genome projects. Their information are usually obtained by experiments and laborious multiple sequence alignment. Based on the fact that motifs are conserved short sequences, we developed method for extracting motifs automatically from pairwise sequence alignment. Moderately similar proteins for a probe protein are searched against all entries in sequence database. Motifs of a probe are then extracted from each pairwise alignment under the specified restrictions. We applied the method to 389 probe proteins from 89 superfamilies in PIR database and evaluated the extracted motifs.