M protein, a major surface protein and virulence factor for the group A streptococcus, exhibits extraordinary size variation in strains of the same serotype (Fischetti et al. 1985). RNA sequence analysis of spontaneous M protein size variants shows that deletion mutations arise in a single strain by homologous recombination events between intragenic tandem repeats. Similar deletion and duplication events also occur in serial streptococcal isolates from a single patient and among related strains in a recent outbreak. We discuss how homologous recombination events can lead to the generation of antigenic variation.