Background: Health information management system has an irrefutable role in raising quality level of treatment and health care. The aim of this study was to compare health information management system in physical medicine clinic of a military hospital and civilian university hospitals in Tehran city. Materials and methods: It is a descriptive cross-sectional survey. The check lists were revised through study in library and hospital information services. A pilot study was performed in a sample hospital to find out the problems of the check lists and then they were distributed among research subjects. Simple random method was carried out in 200 selection patient cases. Results: Findings indicated that the relative frequency of recording information elements present in outpatient cases referring to physical medicine clinic was 71% in military hospital and 69%, 65%, and 50% in other hospitals. Also, the rate of facilities (human resources, place, equipment, and process) was 47% in military hospital and 79%, 58%, and 21% in other hospitals. Conclusion: According to the result of this study, the health information management system facilities, presence of skilled medical record technicians as receptionists, archive and coding disease and fulltime manager is necessary in these clinics. Separated and independent place for reception and archive unit are also required. Equipment (including software and hardware) should be supplied for data entry, data process, and data analysis. It needs to be considered in instructions for documenting and duties of admission unit, archives unit, and director in these clinics.