Background: Although Neisseria gonorrhoeae (Ng) and Chlamydia trachomatis (Ct) are common infections in men who have sex with men, it is unclear from previous studies whether anorectal symptoms are reliable clinical indicators of infection. Aim: The objective of the study was to investigate the clinical significance of questionnaire-elicited or clinically reported anal symptoms for rectal Ng and Ct. Methods: During 2002 to 2003, men who have sex with men (MSM) screened or tested for Ng or Ct according to the national guidelines were invited to participate in a questionnaire. Results: During the study period, 366 MSM were enrolled into the study (88% recruitment rate), of whom 20 (5%) and 25 (7%) were diagnosed with rectal Ng or Ct, respectively. Overall, 'any' anorectal symptoms on a questionnaire were reported equally by those with and without rectal Ng (75 v. 74%, P = 0.69), but heavy anal discharge (P < 0.01) and anal pain (P = 0.04) were more common in those with rectal Ng. Symptoms on the questionnaire were not different among those with and without Ct. Any anal symptoms were reported substantially more often via questionnaire than in a clinical consultation (75 v. 16%, P < 0.01) and symptoms reported in a clinical consultation were not associated with Ng or Ct detection. Conclusion: The weak or absent association between symptoms and the presence of Ct or Ng highlights the importance of annual sexually transmitted infection screening in MSM regardless of symptoms.