Healthcare waste management is an essential field for both researchers and practitioners. Although there have been few studies using statistical methods for its evaluation, it has been the subject of several studies in different contexts. Furthermore, the known precarious practices for waste management in developing countries raise questions about its potential barriers. This study aims to investigate the barriers in healthcare waste management and their relevance. For this purpose, this paper analyses waste management practices in two Brazilian hospitals by using case study and the Analytic Hierarchy Process method. The barriers were organized into three categories - human factors, management, and infrastructure, and the main findings suggest that cost and employee awareness were the most significant barriers. These results highlight the main barriers to more sustainable waste management, and provide an empirical basis for multi-criteria evaluation of the literature.