Background. There are few published reports of research training needs assessments and research training programs. In an effort to expand this nascent field of study and to bridge the gap between research and practice, we sought to systematically assess the research training needs of health care professionals working at Peruvian governmental institutions leading HIV and tuberculosis (TB) control and among senior stakeholders in the field. Methods. Six institutional workshops were conducted with the participation of 161 mid-level health professionals from agencies involved in national HIV and TB control. At each workshop informants completed a structured questionnaire and participated in small and large group discussions. Additional data and institutional commitment was obtained through in-depth interviews from 32 senior managers and researchers from the Ministry of Health, academia and NGOs. Results. Participants exhibited an overwhelming receptivity for additional research training, observing a gap between current levels of research training and their perceived importance. Specialized skills in obtaining funding, developing research protocols, particularly in operational, behavioral and prevention research were considered in greatest need. Beyond research training, participants identified broader social, economic and political factors as influential in infectious disease control. Conclusions. The needs assessment suggests that future training should focus on operational research techniques, rather than on clinical skill building or program implementation only. Strengthening health systems not only requires additional research training, but also adequate financial resources to implement research findings. © 2010 Garcia et al; licensee BioMed Central Ltd.