OBJECTIVE To determine the prevalence of rectal spirochaetosis in homosexual men attending a sexually transmissible diseases clinic and investigate the association between their presence and sexual practices, HIV infection and enteric flora. METHODS The study included 144 male homosexual subjects who each completed a questionnaire, underwent physical examination, proctoscopy and investigations for STD and HIV screening, rectal biopsies and collection of faecal samples. METHODS The Sexual Health Centre, Sydney Hospital, Sydney, Australia. RESULTS Spirochaetes were detected in 39% of the rectal biopsies, using histological criteria. Logistic regression analysis showed that rectal spirochaetosis was significantly associated with: oral-anal contact. (P < 0.05, OR 3.45, 95% CI 1.48-8.05); detection of 3-5 different non-pathogenic protozoa in faeces (P < 0.01, OR 11.68, 95% C.I. 2.33-58) and a positive HIV antibody test (P < 0.01) OR 4.48, 95% C.I. 1.28-15.72). CONCLUSIONS These findings indicate that rectal spirochaetosis is relatively common in homosexual men. The association with non-pathogenic protozoa is most likely attributable to the common mode of transmission viz oral-anal contact. However it is difficult to determine whether the association with HIV infection is cause or effect because of the limitations in the study design. Further information is required to determine the clinical significance of infection with these organisms.