DNA-based assays for typing, and sub-typing, bacteria include genomic restriction profiling (i.e. PFGE), PCR amplification of unique target sequences, genomic microarray hybridization, and sequencing. The first presentation gives a brief introduction into how CFSAN scientists are using two of these approaches to classify different E. coli, Shigella, and Salmonella types. CFSAN scientists have developed a custom Affymetrix microarray with 22K probesets based on known and predicted genes for 28 different E. coli and Shigella serotypes. Results from the validation experiments, where genomic DNA from 13 E.coli and 5 Shigella serotypes was hybridized to the microarray, will be shown. The second example looks at intergenic SNPs in Salmonella Enteridis, which can be used to distinguish serovars that are difficult to resolve with other methods.