The aim of this study was to pilot a practical methodology to assess the condition of sanitation infrastructure and faecal sludge management (FSM) services in order to understand the relative magnitude of the associated environmental health risks. This risk assessment tool was developed as part of the Participatory Rapid Sanitation System Risk Assessment (PRSSRA) methodology which uses local stakeholder knowledge to assess the risks in sanitation chains in order to prioritize interventions to reduce these risks. The tool described in this paper focuses on municipal level sanitary infrastructure which complements the community level risk assessment. The study’s methodology determines the extent of sewerage infrastructure and FSM services, what condition these systems are in, and how they are managed. Through a system of scoring according to criteria that are attributed to health risks, it identifies key weaknesses in the system and critical points where health risks are concentrated. The approach is then used to prioritize the need for interventions and make recommendations for improvement. The paper compares the methodology being piloted against two other approaches that have been developed to assess faecal contamination in low-income settings: SaniPath and Shit Flow Diagram (SFD). This study discusses the merit of using this methodology as a stand-alone tool and including it into SaniPath and SFD in its current or a modified form.