Objectives: Australian guidelines recommend annual testing for HIV and sexually transmitted infections (STIs) for all men who have sex with men (MSM) and 3-6 monthly testing for those at higher risk as defined by behavioural criteria. We assessed HIV/STI re-testing rates among MSM attending primary care clinics. Methods: We conducted a retrospective follow-up of HIV negative MSM tested for HIV or STIs (chlamydia or syphilis) at four primary care clinics in the 9-month period: April to December 2006. Re-testing rates for these infections were calculated over 18 months. Logistic regression was undertaken to identify predictors of guideline adherence. Results: Of the MSM requiring annual HIV testing according to the guidelines, the re-testing rates at 1 y were 35% (762/2163). Among the higher risk MSM, 6-monthly HIV re-testing rates were 15% (283/1862). Within the subgroup who reported 11 or more male sexual partners within the past 6 months, HIV re-testing rates within 6 months were 19%. Independent predictors of HIV re-testing within 6 months in higher-risk MSM were reporting 11 or more male sexual partners in the last 6 months (AOR 3.1, 95% CI 1.8 to 4.8); being born overseas (AOR 2.0, 95% CI 1.2 to 3.4); and previous HIV testing more than 12 months earlier (AOR 3.3, 95% CI 1.9 to 5.5). Conclusion: There is poor adherence to national guidelines that recommend regular re-testing of MSM for STIs, particularly among those at higher risk who require more frequent testing. Clinical strategies are urgently needed to encourage more frequent HIV/STI testing among MSM, especially in the higher risk subgroup.