Selection of the priority tuberculosis (TB) research topics in Peru occurred in three stages: a literature review of TB research findings and information in Peru; proposal of the most important topics by 31 key investigators identified through 233 articles published between 1981 and 2011,16 (48.5%) of the 33 regional coordinators of the National Tuberculosis Prevention and Control Strategy, and influential 16 academics and officials in the area of TB; and a participatory workshop attended by 103 health professionals and officials grouped under 10 thematic discussion groups. Of the 49 research topics identified in the second stage of the process, the 30 most important ones for Peru were selected and prioritized during the workshop. These topics, selected through this inclusive, transparent, and participatory methodology, became the National Tuberculosis Research Agenda in Peru for 2011-2014. These results should help to improve TB control strategies in the country and optimize the use of financial and human resources.