Mycoplasma genitalium is associated with reproductive tract disease in women and may persist in the lower genital tract for months, potentially increasing the risk of upper tract infection and transmission to uninfected partners. Despite its exceptionally small genome (580 kb), approximately 4% is composed of repeated elements known as MgPar sequences (MgPa repeats) based on their homology to the mgpB gene that encodes the immunodominant MgPa adhesin protein. The presence of these MgPar sequences, as well as mgpB variability between M. genitalium strains, suggests that mgpB and MgPar sequences recombine to produce variant MgPa proteins. To examine the extent and generation of diversity within single strains of the organism, we examined mgpB variation within M. genitalium strain G-37 and observed sequence heterogeneity that could be explained by recombination between the mgpB expression site and putative donor MgPar sequences. Similarly, we analyzed mgpB sequences from cervical specimens from a persistently infected woman (21 months) and identified 17 different mgpB variants within a single infecting M. genitalium strain, confirming that mgpB heterogeneity occurs over the course of a natural infection. These observations support the hypothesis that recombination occurs between the mgpB gene and MgPar sequences and that the resulting antigenically distinct MgPa variants may contribute to immune evasion and persistence of infection.Mycoplasma genitalium has been identified as a possible cause of several reproductive tract disease syndromes including urethritis in men and mucopurulent cervicitis, endometritis, pelvic inflammatory disease, and tubal factor infertility in women (3,6,7,18,23,28,30,34,35,41,48,52,55,56). When untreated (or inappropriately treated), this organism persists at infected sites as demonstrated by its association with chronic nongonococcal urethritis in men (22, 53) and its persistence for months, if not years, in the lower genital tract of women (C. R. Cohen, M. Nosek, A. Meier, S. G. Astete, S. Iverson-Cabral, N. R. Mugo, and P. A. Totten, submitted for publication). The longevity of M. genitalium infection in the human reproductive tract suggests that this pathogen may have mechanism(s) to modulate or evade the host immune response.At 580 kb, the M. genitalium G-37 T genome is one of the smallest of any self-replicating cellular organism (9, 17, 49), yet 4% of the fully sequenced genome consists of repeated elements (43) designated as MgPa repeats or MgPar sequences (17). These repeat sequences are so named because they are composed of partial, incomplete copies of the mgpB gene, which encodes the MgPa protein that mediates attachment to various cell types, including the ciliated epithelium of human fallopian tubes (8). Although there is only a single mgpB expression site, there are nine distinct MgPar sequences found throughout the genome (17). The MgPa protein is antigenic and elicits an immune response in animal models (25, 37) and in women with tubal factor infertility (6). The presence...