Genomic sequencing of bacterial pathogens has recently moved from the study of distantly related organisms to within-species comparisons of multiple strains. Strains often differ in their ability to cause disease, and comparative genomics is uncovering novel virulence determinants, hidden aspects of pathogenesis, and new targets for vaccine development. DNA microarrays and other gene-survey techniques are being used to quantify variability in gene content within bacterial populations, and to reveal the strain-specific basis for diversity and severity of pathology.