According to World Health Organization reports, the root of applied researches problems in developing countries are running the researches based on academic researchers ’ interests as well as decision-making in executive systems based on their managers ’ experiences. The problems will be eliminated by stakeholders ’ participation. In 2001, the Community-Based Participatory Research (CBPR) approach was proposed to engage the stakeholders in Iran ’ s research projects. This approach not only would enable the community, but also could change the researchers ’ view on the researches process. It also helps the researchers to apply the researches findings. So, the Population Lab strategy, as a relevant infrastructure to establish CBPR approach, was selected. The strategy was started by 13 Universities of Medical Sciences in Iran. After three years a qualitative research was done to evaluate the stakeholders ’ challenges and obstacles to participate with the population labs. We formed 5 discussion groups and accomplished Focus Group Discussions (FGD) in the groups around five main axes. We collected the stakeholders ’ opinions during the FGDs until data saturation were obtained. According to the data analysis, the most important challenges were distrust, lack of commitment and determination among policy-makers and decision-makers to engage the stakeholders. Besides, the stakeholders ’ mistrust in their role recognition in partnership was one of the main challenges. Since one of the main principles of sustainable and comprehensive development is to employ local methods, it seems lack of a localized model of stakeholders’ participation reduced participation of stakeholders in participatory researches.