To prevent nosocomial outbreaks, elucidation of the source of infection and the mode of transmission is the primary importance. Molecular epidemiology by using DNA fingerprinting and ribotyping is a powerful tool for such analysis, since typing by these methods is based on the whole genome structure. A nosocomial outbreak of Pseudomonas cepacia infection in immunocompromized patients was analyzed by DNA fingerprinting as well as by conventional methods and revealed that the outbreak was associated with contaminated nebulizers. DNA fingerprinting and ribotyping were evaluated with clinical isolates of Pseudomonas cepacia from various sources. Both the methods gave almost identical results, indicating the usefulness of these techniques. Typing by the plasmid profile was reliable only in limited cases. Conventional typing methods such as enzyme typing, bacteriocin typing, phage typing, and serotyping should be used with caution in nosocomial infection, because these are based on phenotypes that are changeable by few genetic events.