BACKGROUND: In countries where STI/HIV prevalence data and behavioural data are scarce UNAIDS second generation HIV surveillance guidelines recommend measuring STI/HIV prevalence and risk behaviours in vulnerable populations but do not recommend conducting these surveys concurrently because of concerns about participation rates, cost, and provision of services. OBJECTIVES: To assess the feasibility of conducting a national combined STD prevalence and behaviour survey in Mali among vulnerable populations with the intention of institutionalisation. METHODS: From March to June 2000 an integrated STI prevalence and behaviour survey was conducted using cluster sampling among five risk groups in four sites in Mali, west Africa. 2229 individuals in non-traditional settings such as taxi/bus stations, market areas, households, and brothels participated in any one or all components of the study: (1) behavioural questionnaire, (2) urine sample for Neisseria gonorrhoeae (GC)/Chlamydia trachomatis (CT) testing, (3) a fingerstick drop of blood for syphilis, and/or (4) HIV testing. RESULTS: High participation rates of 84%-100% were achieved despite specimen collection and HIV testing. Rates fell only slightly when participants were asked to provide biological samples and participants were more likely to provide urine than blood. Rates among the different groups for HIV and syphilis testing are similar and suggest that refusal was most probably because of a reluctance to give blood rather than because of HIV testing. The cost of the biological component added approximately $30 per participant. Included in the $30 are the costs of training, participant services, laboratory personnel and supplies, STI drugs, and STI testing costs. The total cost of the survey was $154,905. Biomarkers aided in validation of answers to behavioural questions. Consenting individuals received HIV pretest and post-test counselling and referral to a trained health provider for treatment of STI and the provision of services provided the framework for interventions in the groups following the survey. CONCLUSION: This represents an effective methodology for collecting risk behaviour and STI/HIV prevalence information concurrently and should be considered by countries expanding STI/HIV surveillance as part of UNAIDS second generation HIV surveillance.