Eighty-two amino acid sequences of the catalytic domains of mature endoxylanases belonging to family 11 have been aligned using the programs MATCHBOX and CLUSTAL. The sequences range in length from 175 to 233 residues. The two glutamates acting as catalytic residues are conserved in all sequences. A very good correlation is found between the presence (at position 100) of an asparagine in the so-called 'alkaline' xylanases, or an aspartic acid in those with a more acidic pH optimum. Four boxes defining segments of highest similarity were detected; they correspond to regions of defined secondary structure: B5, B6, B8 and the carboxyl end of the alpha helix, respectively. Cysteine residues are not common in these sequences (0.7% of all residues), and disulfide bridges are not important in explaining the stability of several thermophilic xylanases. The alignment allows the classification of the enzymes in groups according to sequence similarity. Fungal and bacterial enzymes were found to form mostly separate clusters of higher similarity.