Dealing with health information and taking care of one's own health are key aspects of health literacy and a difficulty for nearly half of the population in Europe. Limited health literacy often results in poorer health outcomes. Health literacy is a fundamental health determinant, and its improvement provides great potential for addressing public health challenges. Health care organizations play an important role in improving population's health literacy. Health literate health care organizations facilitate access, understanding and use of health information and decrease the demands and complexities of the health care system. Few efforts have been taken so far to promote organizational health literacy, especially in German-speaking countries. This project aimed at developing a self-assessment tool, which enables primary care organizations to assess and improve their level of health literacy. The self-assessment tool was developed and evaluated with general practitioners and community care organizations in Switzerland. Here the participative development process, outcomes and the three modules of the self-assessment tool are presented: (1) manual with detailed introduction and instruction, (2) checklist for self-assessment of organizational health literacy and (3) handbook with measures for improvement. The aim of this tool is that organizations are able to identify the need for action, plan and implement improvement measures.