BACKGROUND:The dust and sand storms (DSS) in Iran increased in recent years, which have caused adverse health effects. Regarding the effects of DSS on the health indicators, the health system plays a key role based on the mission and the services which it provides. The present study was conducted, in Iran, to fill the existing knowledge gap and to understand the preparedness challenges of the health system in response to the DSS.MATERIALS AND METHODS:Twenty-one semi-structured interviews, in 2016–2017, were undertaken. This study carried out using purposeful sampling with key informants in the Khuzestan Province, national policymakers in Tehran, as well as people affected by this phenomenon. A qualitative approach, using the conventional content analysis, was employed to analyze the collected data.RESULTS:Four main categories that appear to explain the preparedness challenges of the health system for DSS include the risk assessment, knowledge management, organizational elements, as well as monitoring and evaluation.CONCLUSIONS:It is imperative that policymakers of the country pay special attention to the hazard risk understanding and managing the various aspects of the beliefs and attitudes associated with DSS. The development of early warning system, regular drills and exercises, as well as public and specialized health promotion training related to this phenomenon are suggested.