Motility and chemotaxis are important in the disease process for many species of bacteria. When infected ticks feed, B. burgdorferi moves from the midgut to the salivary gland, and when uninfected ticks feed on infected animals, the spirochete migrates from the animal into the tick. Motility and chemotaxis are likely to be involved in this traveling of B. burgdorferi between the two hosts. Compared with the well-studied Escherichia coli, motility and chemotaxis in B. burgdorferi is quite complex: it has 2 cheA, 3 cheY, 2 cheB, 2 cheR and 2 fliG homologues. Instead of the E. coli phosphatase CheZ, B. burgdorferi has a CheY-P phosphatase called CheX. Furthermore, B. burgdorferi has to coordinate two bundles of periplasmic flagella, extending from opposite ends of the cell, to move toward attractants and away from repellents. B. burgdorferi exhibits different motility modes, consisting of runs, flexes, and reverses, which depend on movement of the bundles of periplasmic flagella. Analysis of the B. burgdorferi genome sequence revealed that it has no homologues of the sigma-28 or anti-sigma factor genes responsible for cascade control of motility gene regulation found in E. coli or Salmonella enterica serovar Typhimurium. Rather, studies indicate that motility genes in B. burgdorferi are regulated by sigma-70 promoters. To determine the role(s) of individual motility genes, we deployed targeted mutagenesis technology and analyzed the resulting cell phenotypes based on the flagellar structure, cell swimming behavior, and effect of specific gene inactivation on other genes and on chemotaxis. Novel functions of many of these genes of the Lyme disease organism are summarized.