The emergence of opportunities for support from the Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM) for HIV-related projects has so far generated funding of over US$75 million for three proposals in Peru. The size of this investment creates the need for close monitoring to ensure a reasonable impact. This paper describes the effects of collaboration with the GFATM on key actors involved in HIV-related activities and on decision-making processes; on health sector divisions; on policies and sources of financing; on equity of access; and on stigma and discrimination of vulnerable and affected populations. Data analysed included primary data collected through interviews with key informants, in-depth interviews and group discussions with vulnerable and affected populations, as well as several public documents. Multisectorality, encouraged by the GFATM, is incipient; centralist proposals with limited consultation, a lack of consensus and short preparation times prevail. No accountability mechanisms operate at the Country Coordinating Mechanism (CCM) level regarding CCM members or society as a whole. GFATM-funded activities have required significant input from the public sector, sometimes beyond the capacity of its human resources. A significant increase in HIV funding, in absolute amounts and in fractions of the total budget, has been observed from several sources including the National Treasury, and it is unclear whether this has implied reductions in the budget for other priorities. Patterns of social exclusion of people living with HIV/AIDS are diverse: children and women are more valued; while transgender persons and sex workers are often excluded. © 2010 Taylor & Francis.