Streptococcus mutans causes dental caries and infective endocarditis. The aim of this study was to determine genomic diversity among serotype c S. mutans laboratory and clinical strains and to characterize the genetic events involved. A genome-based approach using PFGE coupled with Southern hybridization was employed to examine a total of 58 serotype c oral and blood isolates and seven laboratory strains and to compare them with S. mutans UA159. No significant differences were found in the phenotypic characteristics of the strains tested, except that some of the strains exhibited smooth rather than rough colony morphology. In contrast, PFGE profiles of clinical isolates, from either diseased or healthy subjects, exhibited diverse patterns, suggesting that recombination or point mutations occurred frequently in vivo. Diverse PFGE patterns, with various lengths of insertions and deletions, could be detected even within a localized chromosomal region between rRNA operons. Comparative analysis using Southern hybridization with specific markers revealed that a large chromosomal inversion had also occurred between rrn operons in 25 strains.