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To highlight the latest developments in mathematical transmission modelling of HIV epidemics among men who have sex with men (MSM) and people who inject drugs (PWID).Mathematical approaches have been applied to a wide range of topics in recent HIV research. Epidemiological models have evaluated past and forecasted future trends in prevalence and incidence, evaluated innovative behaviour modification strategies and public health programmes aimed at minimizing risk, and explored the potential impact of various biomedical interventions. MSM have developed new risk reduction strategies which models have deemed to be effective at a population level only in certain settings, such as when there are high rates of HIV testing. Modelling has also indicated that persistent circulation of drug-resistant HIV strains is likely to become an inevitable public health issue in the near future in resource-rich settings among MSM. Models have also recently been used to demonstrate that needle and syringe programmes for harm reduction among PWID are effective and cost-effective.Mathematical modelling is particularly amenable to single population groups of concentrated HIV epidemics, such as among MSM and PWID. Models have been utilized to evaluate innovative areas in clinical, biomedical and public health research that cannot be conducted in other population groups. Future directions are likely to include evaluation of specific public health programmes and providing understanding of the importance of specific treatment regimens and incidence and interaction of comorbid conditions associated with HIV.