, the primary etiologic agent of chronic respiratory disease, is a significant poultry pathogen, causing severe inflammation and leading to economic losses worldwide. Immunodominant proteins encoded by the variable lipoprotein and hemagglutinin () gene family are thought to be important for -host interaction, pathogenesis, and immune evasion, but their exact role remains unknown. Previous work has demonstrated that phase variation is dynamic throughout the earliest stages of infection, with 3.03 being the predominant expressed during the initial infection, and that the pattern of dominant expression may be nonrandom and regulated by previously unrecognized mechanisms. To further investigate this gene family, we assessed the profile of two well-characterized vaccine strains, GT5 and Mg7, a 3.03 mutant strain, and an population expressing an alternative immunodominant Here, we report that two vaccine strains show different profiles over the first 2 days of infection compared to that of wild-type R, while the population expressing an alternative immunodominant gene reverted to a profile indistinguishable from that of wild-type R Additionally, we observed a slight shift in the gene expression profile but no reduction in virulence in a 3.03 mutant. Taken together, these data further support the hypothesis that genes change in a nonstochastic temporal progression of expression and that 3.03, while preferred, is not required for virulence. Collectively, these data may be important in elucidating mechanisms of colonization and overall pathogenesis of .