Hospital waste management is an important process that must be dealt with diligently. The management of hazardous waste material requires specific knowledge and regulations and it must be carried out by specialists in the field. In this cross-sectional study, we assessed the main stages of hospital waste management including separation, containment, removal and disposal of waste materials in public hospitals affiliated with Tehran University of Medical Sciences (TUMS). We selected 108 units of six hospitals (three general hospitals and three subspecialty hospitals) from those hospitals supervised by TUMS using the cluster sampling method. The measurement was conducted through a questionnaire and direct observation by researchers. Association analysis was done by statistical tests; Fisher exact test and chi-squared using SPSS software. According to the results obtained by the questionnaire, most of the studied wards scored moderately in terms of quality of their performance in all stages of waste management. About one-fifth of the wards were suffering from poor management of their medical waste and only a minority of wards obtained good scores for managing their waste materials. The findings also revealed significant associations between temporary waste storage and collection and the level of education of the managers (P = 0.040, P = 0.050, respectively). In summary, the study indicated a moderate management in all processes of separation, collection, containment, removal and disposal of waste materials in hospitals with several observed problems in the process.