Venereal lymphogranuloma (VLH) is a sexually transmitted infection (STI) caused by highly invasive serovariants of Chlamydia trachomatis (C. trachomatis) L1, L2 and L3. Since 2003, in Europe, North America, and Australia, outbreaks of the infection have been reported that have occurred exclusively among men who have sex with men (MSM), with clinical presentation of proctitis and proctocolitis of varying severity in more than 90% of cases. In this regard, it should be noted that VLH should be differentiated from symptoms of inflammatory bowel disease (IBD) with rectal involvement. A distinct feature of rectal VLH is the severity of symptoms, which progress rapidly without causal treatment. There are no reports of rectal VLH cases in the domestic professional literature. We have presented a case of rectal VLH for the first time in the Russian Federation. The clinical presentation was fully consistent with the symptoms of IBD with rectal involvement. The diagnosis was confirmed by fibrocolonoscopy. However, medical history data, peculiarities of patients’ sexual practices, and pathomorphological findings of rectal mucosa biopsy specimens did not reliably confirm the IBD. Reports in the foreign literature of VLH cases in MSM were not taken into account in the diagnostic search. Treatment with mesalazine was ineffective. Using additional PCR tests for detection of VLH pathogen DNA, the definitive diagnosis was established, and the administered antibiotic therapy led to a favorable outcome.