BACKGROUND Since 1999 there has been an increase in the number of HIV diagnoses in Australia, predominantly among men who have sex with men (MSM), but the magnitude of increase differs between states: approximately 7% rise in New South Wales, approximately 96% rise in Victoria, and approximately 68% rise in Queensland. METHODS Epidemiological, clinical, behavioural and biological data were collated into a mechanistic mathematical model to explore possible reasons for this increase in HIV notifications in MSM. The model was then used to make projections to 2015 under various scenarios. RESULTS The model suggests that trends in clinical and behavioural parameters, including increases in unprotected anal intercourse, cannot explain the magnitude of the observed rise in HIV notifications, without a substantial increase in a 'transmission-increasing' factor. We suggest that a highly plausible biological factor is an increase in the prevalence of other sexually transmissible infections (STI). It was found that New South Wales required an approximately 2-fold increase in other STI to match the data, Victoria needed an ~11-fold increase, and Queensland required an approximately 9-fold increase. This is consistent with observed trends in Australia for some STI in recent years. Future projections also indicate that the best way to control the current rise in HIV notifications is to reduce the prevalence of other STI and to promote condom use, testing for HIV, and initiation of early treatment in MSM diagnosed during primary infection. CONCLUSIONS Our model can explain the recent rise in HIV notifications with an increase in the prevalence of other STI. This analysis highlights that further investigation into the causes and impact of other STI is warranted in Australia, particularly in Victoria.