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Background: The global population has grown and is still growing. This growth is happening in more cities than in rural areas, given the continual search for economic opportunities. The implication of this growth is the growth of healthcare centers to meet the growing healthcare demand. Accordingly, healthcare waste production has posed a big challenge to health waste disposal and management. Objectives: This study aimed to prioritize and select the best method of waste management in the health sector with multi-criteria decision making (MCDM) approaches. Methods: The present cross-sectional study was carried out to select the best method of managing healthcare wastes through MCDM approaches in Qazvin. The sample was selected and assigned to two groups of 28 experts (five categories) who evaluated the criteria and a group of 22 individuals (four categories) to rank disposal methods of healthcare waste. First, six waste disposal methods and 12 criteria for designing a questionnaire were identified. After designing the questionnaire, the analytic hierarchy process (AHP) was used to calculate the weights of the criteria. Then, the TOPSIS method was used to rank different waste disposal methods. We used EC (ver. 8), Excel (Microsoft, 2007), and Lingo (ver. 14) for analyzing the data. Results: Concerning the rank of health waste disposal methods based on common existing criteria, urban and rural areas should use different disposal methods. The best disposal methods are irradiation (0.839) and microwave (0.794) in urban areas and steam sterilization (0.867) and microwave (0.840) in rural areas. In both areas, incineration was ranked the last. Conclusions: To achieve the effective disposal and safety of health waste in urban and rural areas, varied but applicable disposable methods should be used for the management of health waste disposal.