Objectives To determine the prevalence of anorectal Chlamydia trachomatis serovars in a group of men who have sex with men (MSM) with high risk sexual behaviour, attendees at a sexually transmitted infection (STI) unit from a region in Northwest Spain.

Design Retrospective and descriptive study of all swabs obtained from all MSM attendees at an STI unit, from 2007 to 2011. Retrospective ethical approval was granted by the Ethical Regional Committee of Clinical Investigation of the Principality of Asturias.

Setting The STI clinic in Oviedo, Spain, offers screening and free-of-charge treatment to about 3646 patients per year.

Participants 303 symptomatic and asymptomatic consecutive and unselected MSM patients (mean age 36.7 and range 21–55 years) were evaluated for anorectal chlamydial infection.

Main outcome measures C trachomatis DNA extraction and detection in all rectal and in 36 urethral swabs. Characterisation of C trachomatis genotypes through sequencing of ompA gene amplicons and further phylogenetic tree analysis.

Results We found 40 (13. 2%) positive rectal samples. The distribution of genotypes was E (37. 5%) followed by G (25%), D (12. 5%), J (10%) and L2b (5%).25 (62.5%, 95% CI 46.2 to 78.7) of the chlamydia-infected MSM showed clinical manifestations while 15 (37.5%, 95% CI 21.25 to 53.75) reported no symptoms. Concurrent infection with other STIs was documented in 27 (67.5%, 95% CI 51.7 to 83.2) patients. The most frequently reported clinical symptom was anal ulcer (7 cases, 17.5%; 95% CI 4.47 to 30.52). E genotype was mostly detected in asymptomatic patients. There were non-E genotypes detected in 21 (84%, 95% CI 63.9 to 95.5) of 25 symptomatic patients (p<0.001).

Conclusions The first two confirmed cases of lymphogranuloma venereum (LGV) in MSM in Asturias are reported, probably indicating the increase of this infection. The Spanish C trachomatis laboratory-based surveillance system may underlie an underestimated number of chlamydial infections. Whenever mild and atypical symptoms exist, laboratory evaluation would contribute to the early implementation of appropriate therapy and prevent LGV dissemination.