Background: Chlamydia is the most commonly notified sexually transmitted infection (STI) in Australia. Incidence studies of chlamydia in men who have sex with men (MSM) are rare and offer important public health information. Objective: To determine chlamydia incidence in MSM presenting at high caseload clinics and describe predictors of infection. Methods: The Victorian Primary Care Network for Sentinel Surveillance of bloodborne viruses and STIs (VPCNSS) links testing, demographic and behavioural data from individual testers at participating clinics. Data from MSM with more than one chlamydia test at the VPCNSS site between April 2006 and June 2010 were included. Chlamydia incidence per 100 person-years (PY) was calculated and Cox regression used to examine predictors of incidence. Results: 1206 positive tests for chlamydia were detected among 6333 MSM across 11 409 PY of followup. Overall chlamydia incidence was 10.6/100 PY (95% CI 10.0 to 11.2) and was highest among MSM aged 16-29 years (12.9/100 PY, 95% CI 11.7 to 14.1), presenting with STI symptoms (16.0/100 PY, 95% CI 14.2 to 18.0), HIV positive (18.5/100 PY, 95% CI 16.6 to 20.6) and self-identified sex workers (14.3/100 PY, 95% CI 10.0 to 20.6). Significant predictors of chlamydia infection among MSM were younger age (adjusted hazard ratio (aHR)=1.9, 95% CI 1.5 to 2.3), self-identifying as a sex worker (aHR=1.6, 95% CI 1.0 to 2.6), being HIV positive (aHR=2.6, 95% CI 1.8 to 3.8), presenting with STI symptoms (aHR=1.7, 95% CI 1.4 to 2.1) and reporting >10 sex partners in the past 6 months (aHR=2.5 95% CI 1.4 to 4.6). Conclusion: These results show that MSM represent a key risk population for chlamydia in Australia and identify a number of high-risk MSM subpopulations for whom clinical and public health interventions are warranted.