Ribotyping and macrorestriction analysis of chromosomal DNA using pulsed-field gel electrophoresis (PFGE) are among the more useful molecular epidemiologic typing methods. Because these techniques are labor intensive, automation of one or more steps may allow clinical laboratories to apply molecular typing methods. We compared the recently developed automated ribotyping system, the RiboPrinter Microbial Characterization System (DuPont), with PFGE as a means of typing clinical isolates of E. coli and P. aeruginosa. A total of 22 E. coli and 24 P. aeruginosa were typed by both PFGE and the RiboPrinter. When compared with PFGE typing of E. coli and P. aeruginosa, the RiboPrinter was less sensitive in identifying different strains, particularly among the isolates of P. aeruginosa. The RiboPrinter was completely automated and allowed up to 32 isolates to be typed within an 8-hour period. The pattern of results obtained in this study suggests that a heirarchical approach to molecular typing using the RiboPrinter Microbial Characterization System plus PFGE might be feasible. The RiboPrinter Microbial Characterization System promises to be a very useful addition to the expanding molecular typing armamentarium.