While it stands to reason that L-serovars of C. trachomatis has been present within the U.S. population for some time, efforts to assess the prevalence of the disease have been hampered by slow, complex diagnostic methods. The increasing use of real-time PCR as a clinical and public health tool has facilitated the detection of specific chlamydial strains. We have applied real-time PCR to the detection of L-serovar C. trachomatis in an effort to survey for the organism within the city and county of San Francisco. We found that L-serovar C. trachomatis was routinely detectable in rectal-positive C. trachomatis specimens.