Background: Rising trend of emergencies and disasters in the world has caused a lot of damage to the health care facility infrastructures. This has led the health needs of the affected population to be the first and most requirement in emergencies and disasters. In most countries for the timely and appropriate response to the health needs of the affected areas, structured and organized teams are formed. Given the frequent occurrence of events in Iran and the adverse effects of emergencies and disasters on the community health, this study aimed to investigate the obstacles and challenges associated with the organization and preparation of Iran’s Emergencies and Disasters Medical Response Teams (EDMRT). Materials and Methods: In this study, a qualitative approach with a content analysis method was used to explore and extract the obstacles and challenges of the medical response teams in the field of organization and preparation. Data collection was done through 18 in-depth, unstructured, and semi-structured interviews with 16 experts and experienced people who were purposefully selected. Besides the interview, field visits and related reports were used to confirm or reject the findings. Data analysis was done by the qualitative approach recommended by Graneheim. Results: The obstacles and challenges associated with the organization and preparation of teams were obtained under 1 theme, 2 categories, and 10 subcategories. The main theme was “team management”. The categories included unorganized groups and frangible readiness. Concepts of the team; unknown structure, lack of effective leadership/command, poor supervision of proctor organization, membership; complex process, heterogeneous composition are the sub-categories related to the first category. And concepts of local level; disable to establishment a team; disaster medicine, unfamiliar concept; lack of air care team; dependence versus self-sufficiency; non-systematically support; and inappropriate location of deployment are the sub-categories of the second category Conclusion: The results of the study show that the current structures for medical response in emergencies and disasters have numerous challenges in terms of organization and preparedness. This defect harms the performance and effectiveness of medical response teams and an obstacle to the overall policy of reducing damages in disasters. The present study illustrates the need to review and refine the organization and preparedness processes associated with the current structure of medical response teams in emergencies and disasters. Of course, it is recommended that a more comprehensive study be conducted to identify and address the other areas of influence in these teams, such as legal considerations, health and safety, and related security issues.