Sixteen clinical Vibrio cholerae O1 strains from four different countries were selected for comparison by traditional ribotyping and an automated RiboPrinter™ system for identification and discrimination purposes. Automated ribotyping, which routinely uses the restriction enzyme EcoRI for typing all bacterial species, produced only five different ribotypes compared with 10 different EcoRI ribotypes obtained by the traditional method. Traditional and automated ribotyping using the restriction enzyme BglI, which is recommended for the ribotyping of V. cholerae, produced 10 and seven different ribotypes, respectively. The lower discrimination shown by the RiboPrinter™ system was caused mainly by an inability to differentiate closely located fragments due to a lower resolution and electrophoresis conditions, a parameter which cannot be changed in the automated system. The RiboPrinter™ system includes a database for bacterial identification. However, none of the V. cholerae O1 strains studied showed EcoRI ribotype patterns which matched any of the patterns included in the database. In conclusion, the existing RiboPrinter™ system is not adequate for taxonomic identification and classification of V. cholerae O1.