Infection control teams rely on microbiology laboratories for accurate, reproducible data to trace the spread of microorganisms in the hospital. Since few problems are recognized immediately, laboratories should save important nosocomial pathogens so that outbreak strains will be available for analysis by more sophisticated techniques, particularly since automation has reduced the amount of epidemiologically useful data generated by routine procedures. Traditional supplemental reference procedures include phage typing, biotyping, serotyping and bacteriocin typing. Recently, analysis of antibiotic resistance determinants has provided the hospital epidemiologist with additional tools. Resistant strains have been characterized by their production of specific antibiotic inactivating enzymes. Agarose gel electrophoresis and restriction endonuclease analysis of plasmid DNA have permitted precise characterization of nosocomial strains, and the spread of antibiotic resistance genes can now be followed by sensitive and specific DNA probes. DNA probes also show promise for distinguishing nosocomial strains bearing known virulence factors from strains with less pathogenic potential. Molecular genetics techniques have found an additional role in elucidating the epidemiology of nosocomial viruses, especially the herpesviruses.