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OBJECTIVES: To establish a new mechanism for monitoring patterns of HIV infection, in the context of a sustained increase in HIV diagnosis among men who have sex with men (MSM) in Victoria. METHODS: Between April 2004 and August 2005, a linked voluntary HIV sentinel surveillance system was implemented at five medical clinics with a high case load of MSM. Using a questionnaire, doctors collected HIV testing history, demographic and sexual risk behaviour information from all clients undergoing voluntary HIV testing. Questionnaires were linked with HIV test results. Logistic regression analysis was conducted to determine factors associated with HIV infection. RESULTS: Of 3435 MSM tested for HIV at participating sites, 1.7%, (95% CI = 1.2-2.2) were newly diagnosed with HIV; between 2004 and 2005 the proportion increased from 1.3% (95% CI = 1.2-1.5) to 2.0% (95% CI = 1.8-2.2), P = 0.107. There was no significant change in the number of HIV tests conducted per month or in demographic characteristics, testing history and sexual behaviour characteristics between time periods. In multivariate analysis, reporting unprotected anal intercourse (UAI) with any partner, UAI with a HIV-positive partner/s and being aged 30-39 years or 40 years or greater were significantly associated with HIV infection. CONCLUSION: This new surveillance mechanism, based on linked testing at participating clinics, indicates that the increase in HIV notifications in 2005 was unrelated to changes in testing and data from a Melbourne sexual behavioural survey suggests the increase was more likely to be attributed to increases in transmission within the past few years. The sentinel system highlighted UAI, especially with HIV positive partner/s are important transmission factors.