Vibrio cholerae, the causative organism of the human disease cholera, is a highly motile polarly flagellated bacterium, and motility has been implicated as a virulence determinant, but the exact connection between motility and virulence is still unclear. Transcription profiling of V. cholerae strains with mutations in the flagellar regulatory hierarchy utilizing whole genome microarrays revealed increased expression of genes encoding proven and putative virulence factors, including cholera toxin, the toxin co-regulated pilus, hemolysins, and adhesins. Phenotype microarrays revealed that carbon source utilization of flagellar mutants is altered, demonstrating that metabolic pathways are also controlled by the flagellar hierarchy. We have identified a specific hemolysin negatively regulated by the flagellar hierarchy that is responsible for lysis of human O red blood cells. We have also identified a hemagglutinin responsible for agglutination of human O red blood cells that is positively regulated by the flagellar hierarchy. The flagellar-regulated hemagglutinin (FRH) is an RTX-like protein that also mediates binding to chitin and human epithelial cells, and biofilm formation. A frhA mutant strain is defective for intestinal colonization, utilizing the infant mouse model of cholera. The flagellar hierarchy regulates frh gene expression via a GGDEF protein, through modulation of cyclic diguanylate levels. Further study revealed that FrhA depends on the presence of calcium for its function, indicating that cadherin repeats present in FrhA might be responsible for the FrhA-mediated binding properties of V. cholerae. We have identified a novel Type I secretion system that is involved in FrhA secretion. Our studies have demonstrated that the flagellar hierarchy controls expression of a large number of non-flagellar genes that impact the virulence of V. cholerae.