Antiretroviral treatment (ART) for those infected with HIV can prevent onward transmission of infection, but biological efficacy alone is not enough to guide policy decisions about the role of ART in reducing HIV incidence. Epidemiology, economics, demography, statistics, biology and mathematical modelling will be central in framing key decisions in the optimal use of ART. PLoS Medicine, with the HIV Modelling Consortium, have compiled a set of articles that draws together reactions to the new findings from these perspectives with a forward-looking research agenda. Interlocking themes across those articles are described here. We hope that this collection of articles will provide a foundation upon which greater collaborations between disciplines will be formed, affording deeper insights into these factors that will strengthen the support for evidence-based decision-making in HIV prevention.