Background: Inasmuch as accreditation is of great significance for hospitals, this study aimed to explain the accreditation challenges of Iranian hospitals through a content analysis approach. Methods: A qualitative study was run through the content analysis method in 2018. 19 semi-structured interviews were conducted with experts and data were saturated. To increase the accuracy and precision of the study, Guba and Lincoln’s four criteria including credibility, dependability, conformability and transferability were used. MAX QDA 10 was used for data analysis via 5-step framework analysis approach. Results: The findings identify 5 main themes and 29 subthemes. The main themes included macro and policy making issues, evaluators' issues, structures and processes, executive issues, and accreditation measures. The macro policy making issues include: non-alignment of accreditation policies, waste of resources, lack of independent organization for accreditation, ignoring the stakeholders and contradictory regulations. Evaluators issues contain: shortage of evaluators, high current expenditures of evaluators, lack of motivation, irrelevancy of evaluators' expertise, conflict of interest and irregular and tight schedules of evaluations. Structural and process challenges involve: ignoring the infrastructures, unstandardized old hospital buildings, lack of competition between hospitals, Inconsistency of hospitals` strategic plan and instrumental use of accreditation by hospitals. Executive issues comprise high workload and dissatisfaction, lack of attention to main tasks, staff resistance against accreditation, lack of physicians` involvement and its time-consuming nature. And finally the last theme, Accreditation measures consist: Interference and parallel measures, ambiguity and unclearness of measures, using the same measures for different hospitals, weakness of measures, uniform weight of measures, inappropriate structure of scoring and failure to revise the measures. Conclusion: The results shed light on the fact that Iranian hospitals need to experience major changes in applying accreditation as a quality assurance mechanism. In other words, it seems necessary for policy makers affiliated with Ministry of Health and Medical education to revise accreditation measures according to hospital needs and try to clarify the structure and executive process of the accreditation. Moreover, improving and standardizing the evaluators` skills is recommended.