Background Several lymphogranuloma venereum (LGV) outbreaks among men who have sex with men (MSM) have been reported throughout the world since 2003. Nevertheless, no LGV cases have been internationally reported from Russia. We evaluated the prevalence of LGV among MSM attending proctologists in Moscow, Russia, and compared the LGV and non-LGV rectal Chlamydia trachomatis (CT) infections. Methods MSM ( n = 534) attending for proctologic care were included. Rectal specimens were sampled for CT and Neisseria gonorrhoeae (NG) by nucleic acid amplification tests (NAATs). All CT-positive patients were tested with an LGV-specific NAAT. Results In total, 37.3% (95% CI 33.3–41.5; 199/534) of MSM were CT positive. Of these, 68.8% (95% CI 62.1–74.9; 137/199) had LGV and 31.2% (95% CI 25.1–37.9; 62/199) a non-LGV rectal CT infection. Older age (34 years vs. 31 years, p = 0.035) and group-sex practices (67.2% (92/137) vs. 33.9% (21/62), p < 0.0001) were associated with LGV. The LGV-positive MSM were also more likely to be HIV-positive (67.2% (92/137) vs. 41.9% (26/62), p = 0.001). Proctoscopy revealed ulcerative proctitis/proctocolitis in 99.3% (136/137) of LGV-positive MSM. No ulcerative or erosive proctitis was found in the MSM with non-LGV CT infection, but 58.1% (36/62) of them had anorectal disorders. Finally, mild catarrhal or hemorrhagic proctitis was diagnosed in only 21.6% (8/37) of MSM with non-LGV CT infection lacking concomitant NG or syphilis ( p < 0.0001). Conclusions LGV is widely spread among MSM attending proctologists in Moscow. Clinically, acute LGV proctitis/proctocolitis can be difficult to distinguish from inflammatory bowel disease that leads to mismanaged LGV infections. LGV diagnostic laboratory testing is essential, however, currently mainly lacking for MSM in Russia. All MSM with CT-positive rectal specimens should be subsequently tested for LGV.