Background: Syphilis has re-emerged and become established in gay communities in most developed countries since the late 1990s. HIV infected men have been disproportionately affected by this endemic, but it is unclear whether this is due to behavioural or biological reasons. We report incidence and risk factors for syphilis in two community-based cohorts of HIV-negative and HIV-positive homosexual men in Sydney, Australia. Methods: Participants were recruited using similar community-based strategies in both cohorts and underwent annual face-to-face interviews. Syphilis screening was offered to all consenting participants at annual visits. Results: In the HIV-negative cohort, 21 men seroconverted to syphilis and one man had a syphilis re-infection during 2001–07, an incidence of 0.49 per 100 person-years (95% CI: 0.31–0.74). In the HIV-positive cohort during 2005–07, eight men seroconverted and one man had a syphilis re-infection, giving an incidence of 3.62 per 100 person-years (95% CI: 1.67–6.48). All nine reported a recent CD4 count of more than 350 cells µL–1. Syphilis incidence was significantly higher in the HIV-positive cohort after adjustment for age (hazard ratio (HR) = 9.20, 95% CI: 3.63–23.31). Unprotected anal intercourse (UAI) with HIV-positive partners was significantly associated with incident syphilis in both cohorts (HR = 4.45, 95% CI: 1.37–14.45 in HIV-negative; HR = 8.67, 95% CI: 1.03–72.76 in HIV-positive). Conclusion: Syphilis incidence was almost 10-fold higher in HIV-positive than in HIV-negative homosexual men, and it was not related to a CD4 count below 350 µL–1. UAI with HIV positive partners was of particular importance in the transmission of syphilis.