During the screening of a Staphylococcus aureus signature-tagged mutagenesis library, it was noted that nonhemolytic bacteria became more abundant as time passed in murine abscess and wound models, but not within organ tissues associated with systemic infections. To examine this further, a mixed population of hyperhemolytic, hemolytic, and nonhemolytic S. aureus strain RN6390 cells were inoculated into mice using abscess, wound, and systemic models of infection. After 7 days in the abscess, the hyperhemolytic group markedly declined, whereas the nonhemolytic population increased significantly. A similar phenomenon occurred in murine wounds, but not during the systemic infection. Sequencing of several of the signature-tagged mutants indicated mutations in the agrC gene or within the agrA–agrC intergenic region. Both α-hemolysin and δ-hemolysin activity was curtailed in these mutants, but β-hemolysin activity was unaffected. Single strain comparisons between wild-type strain 8325–4 and strain DU1090 (hla-) as well as between strain RN6911 (agr) and wild-type strain RN6390 were performed using the same three animal models of infection. The agr mutant strain and the hla mutant strain showed no difference in bacterial counts in murine wounds compared to their respective parent strains. The same held true in murine abscesses at day 4, but strain RN6911 counts then declined at day 7. Considerable clearing of the hla mutant strain and the agr mutant strain occurred in the systemic model of infection. Mixed infections with the DU1090 and 8325–4 strains in the abscess model showed a slight advantage given to the DU1090 population, but a distinct selection for the parental 8325–4 strain in the liver. These results suggest that agr mutations cause reductions in the expression of several secreted proteins, including α- and δ-hemolysin, which in turn contribute to a growth advantage of this agr mutant group within a mixed population of S. aureus cells residing in abscesses and wounds.