The human pathogen Chlamydia trachomatis exists as multiple serovariants that have distinct organotropisms for different tissue sites. Culture and epidemiologic data have demonstrated that serovar G is more prevalent, while serovar E is less prevalent, for rectal isolates from men having sex with men (MSM). The relative prevalence of these serovars is the opposite for isolates from female cervical infections. In contrast, the prevalence of serovar J isolates is approximately the same at the different tissue sites, and these isolates are the only C-class strains that are routinely cultured from MSM populations. These correlations led us to hypothesize that polymorphisms in open reading frame (ORF) sequences correlate with the different tissue tropisms of these serovars. To explore this possibility, we sequenced and compared the genomes of clinical anorectal and cervical isolates belonging to serovars E, G, and J and compared these genomes with each other, as well as with a set of previously sequenced genomes. We then used PCR-and restriction digestion-based genotyping assays performed with a large collection of recent clinical isolates to show that polymorphisms in ORFs CT144, CT154, and CT326 were highly associated with rectal tropism in serovar G isolates and that polymorphisms in CT869 and CT870 were associated with tissue tropism across all serovars tested. The genome sequences collected were also used to identify regions of likely recombination in recent clinical strains. This work demonstrated that whole-genome sequencing along with comparative genomics is an effective approach for discovering variable loci in Chlamydia spp. that are associated with clinical presentation.Chlamydia trachomatis is an obligate intracellular human pathogen that is the leading cause of preventable blindness worldwide and is the most common sexually transmitted infectious bacterium in humans. The study of the biology of chlamydiae is complicated by their obligate intracellular development and the lack of a routine system for directed mutagenesis. Chlamydial isolates are differentiated into serovars based on serospecificity for the chlamydial major outer membrane protein (MOMP) (7), which is encoded by ompA (37). The serovars fall into biological groups associated with trachoma (serovars A to C), sexually transmitted noninvasive disease (serovars D to K), and invasive lymphogranuloma (serovars L1 to L3) (35). Comparative genomic analysis of ocular and urogenital chlamydial species has proven to be an effective approach for discovering genetic loci that are associated with observed tissue tropism (9, 10).Studies conducted in Seattle, WA, and Birmingham, AL, have shown that serovar G rectal isolates are prevalent in men having sex with men (MSM), while serovar E rectal isolates are less prevalent (1,5,17). This prevalence of serovar G and rectal tropism differ from what has been observed in studies of female cervical populations in the same geographical regions, where the prevalence of serovar E was significantly higher than the pre...