High resolution AFLP fingerprinting, in which subsets of genomic restriction fragments are amplified by means of PCR, was used for the identification of different Salmonella serotypes to investigate whether this technique is applicable in epidemiological studies. Seventy-eight different Salmonella strains comprising 62 serotypes were genetically identified by AFLP. Primer combination M00 (MseI primer without additional 3′ nucleotides) and E11 (EcoRI primer with two additional 3′ nucleotides) resulted in reproducible profiles containing approximately 50 bands. All serotypes were characterized by a unique profile. In addition, AFLP fingerprinting enabled phage type identification. Different strains previously identified as identical, using typing methods with lower resolution, could be distinguished, showing that AFLP fingerprinting is well suited for bacterial epidemiology and identification.