OBJECTIVES: Sexually transmitted infections (STIs) such as anal/genital warts, syphilis and genital/rectal gonorrhoeal/chlamydial infections compromise the health of men who have sex with men (MSM). Rectal bacterial STIs increase the per-contact risk of HIV infection. Early detection of asymptomatic STIs requires regular screening including collection of clinical specimens (or, for warts: physical examinations) that allow for the detection of infections at sites common to men's same sex practices. METHODS: From June to August 2010, the European MSM Internet Survey recruited 174,209 men from 38 European countries to an anonymous online questionnaire in 25 languages. As sexual healthcare for MSM in most countries is organised locally, we chose cities for comparison. Multivariable regression models were used to compare accessibility of services and applied diagnostic procedures across 40 cities. RESULTS: The proportion of respondents tested for STIs in the last 12 months in the absence of symptoms ranged from 8.9% in Istanbul to 48.0% in Amsterdam. At city level, low STI screening correlated with inaccessible services (R2=44.1%). At individual level, anal/penile inspection and anal swabbing was most common in U.K. cities, Amsterdam, Dublin and Stockholm. Compared to London, MSM in 30 cities had an adjusted OR (AOR) of (0.02 to 0.18) for anal swabbing; and (0.06 to 0.25) for anal/penile inspection (p<0.001). CONCLUSIONS: Anal/genital warts and rectal infections are likely to be profoundly underdiagnosed among MSM in most European cities. This has implications for the sexual health of MSM, HIV prevention and comparing national surveillance data. There is an urgent need to improve sexual healthcare tailored to MSM at risk for STIs.