Molecular typing methods are capable of providing detailed strain characteristics which are commonly far beyond the capacities of phenotypic typing methods. Such molecular-based characteristics have proved to be very helpful in epidemiological studies of bacterial pathogens. The primary criteria that all typing methods should fulfill include (1) the typeability of the strains in question, (2) the reproducibility of the results, and (3) a high discriminatory power. In general, molecular typing methods can be differentiated with regard to their use in methods that can be applied to virtually all bacteria (e.g. plasmid profiling, ribotyping, macrorestriction analysis) and methods which can only be used for typing of certain bacterial genera or species (e.g. IS200 typing of certain Salmonella enterica subsp. enterica serovars, or coa-PCR of coagulase-positive staphylococci). In the present review, various phenotypic and molecular methods for the epidemiological typing of bacteria of the genera Staphylococcus, Salmonella, and Pasteurella are described and their advantages/disadvantages--also with regard to the fulfillment of the above-mentioned primary criteria--are critically assessed.