Borrelia burgdorferi is a member of a cluster of closely related spirochete species, which also include B. garinii, B. afzelii, B. japonica, B. andersonii and several as yet unnamed types (Casjens et al., 1995, Marconi et al., 1995 and references therein). This group is called the “Lyme Borrelias” or “Lyme disease agents,” even though only B. burgdorferi, garinii and afzelii are currently known to cause Lyme disease. The 945±10 kbp chromosomes of all these bacteria are linear, and genetic maps of the chromosomes from each of these species are very similar (Ojaimi et al., 1994; Casjens et al., 1995). The map of the chromosome of B. burgdorferi isolate Sh-2–82 is shown in Figure 52-1. To date, 34 gene clusters have been mapped to various restriction site intervals. These clusters contain 68 genes which are either known to be expressed in B. burgdorferi or have strong homology to genes whose function are known in other systems, as well as 11 complete open reading frames of unknown function.