Introduction & Objective: Today, the use of information technology (IT) has had positive impact on health systems, especially in the field of disease control, diagnosis, patient management and education. But despite the various developed applications of IT in all aspects of clinical and increase confidence and efficiency, this technology is not yet fully penetrate in medical and treatment field and there are many challenges and obstacles in accepting and applying it. Accordingly, this study examined challenges of IT applications in hospitals affiliated with Shaheed Beheshti University of Medical Sciences.Materials & Methods: Current research is descriptive-applied. Data were collected using two structured questionnaires and by viewing systems and documents and interviewing with managers of IT in 5 teaching hospitals. Compiled data were examined by SPSS software by using descriptive statistics.Results: Based on findings, from 14 areas of IT applications, all hospitals have electronic medical records but not fully formed, 3 hospitals have picture archiving system, 2 hospitals have community based health information networks, and answering phone and only one of them has e-complaints system, Physician-Hospital data network and data processing service.All IT managers noted advancing in computer technology as a stimulating factor and medical processes, business processes and economic factors as obstacles in applying IT in their hospitals. Also, 4 hospitals noted, the professional structure, and 3 hospitals noted the human factors as stimulating factors in the acceptance and use of IT.Conclusions: Based on the results, fields and the capabilities of applying IT, areas of influence and the obstacles facing the development of IT from professionals and senior information managers' view were identified. Thus, the factors influencing the policy making of these hospitals in IT applications was specified factors which can provide grounds for use of the efficient hospital resources, and thus cause cost reduction and downsizing care of services and therefore can create new employment opportunities for health care workers.Also, in prioritizing the macro-level budget in Ministry of Health, it can be considered as a basis for investment in hospital IT policies.