Amplified fragment length polymorphism (AFLP) is a powerful PCR-based fingerprinting method and has the capacity to reveal variation around the whole genome by selectively amplifying a subset of restriction fragments for comparison. The restriction fragments analyzed are small, and even mutation of 1 bp can be detected. The use of different sets of restriction enzymes or different primer combinations can generate large numbers of different AFLP fingerprints. AFLP is of particular value for studies of closely related strains, such as analysis of variation within a serovar of Salmonella enterica. We present here protocols for both radioactively labeled and fluorescent dye-labeled AFLP analyses that are also applicable to other bacterial species. Fluorescent AFLP has proved to be reproducible and capable of standardization.