Filtration and prioritization are two basics steps in horizon scanning systems. This article aimed to map stakeholders' preferences in the Brazilian Unified National Health System (SUS) regarding filtration and prioritization criteria. Two filtration criteria (time horizon and innovation) and eight prioritization criteria (relevance to epidemiology, health policies, and clinical practice; potential impact on SUS budget, healthcare providers' costs, and mortality; safety; and legal, ethical, and social aspects) were selected. Multiple correspondence analysis was used to map stakeholders' preferences within and between groups. Two groups were more homogeneous and determinant for selection of prioritization criteria. Stakeholders' professional experience had more influence than institutional affiliations. The approach showed transparent criteria selection and analysis of stakeholders' individual preferences.