The legislation reauthorizing the President's Emergency Plan for AIDS Relief (PEPFAR) in 2008 recognized the need for HIV/AIDS programs directed to most-at-risk populations, including men who have sex with men and people who inject drugs. To examine whether that goal is being met, we analyzed data from PEPFAR's Operational Plans for fiscal years 2009 and 2010. The eighteen countries in our study accounted for nearly two-thirds of overall PEPFAR financing for those fiscal years and approximately 60 percent of the total number of people living with HIV in the world in 2010. After controlling in each country for the number of people living with HIV, total population, and per capita income, we found that countries where HIV transmission occurs primarily among men who have sex with men and people who inject drugs received on average $235 million less in 2009 and 2010 than countries with widespread HIV epidemics among the general population. These findings raise questions about whether the country allocations of PEPFAR fully address needs based on the epidemiology of HIV infection in individual countries. Administrators should ensure that funding allocations directed to various countries reflect the best epidemiological data and latest science and best practices, and are devoid of bias against most-at-risk populations; they should also be more transparent about where PEPFAR's dollars go. Otherwise, it is unlikely that PEPFAR will realize its established goal of achieving an AIDS-free generation.