This document presents a conceptual framework for integrated assessment of human and animal waste. The framework has three main components: health status, physical environment, and socio-economic environment. Various disciplinary methods are used to obtain information on each component. Analyses characterize health, ecological and social risks while identifying critical control points. Interventions consider biomedical, engineering and social science perspectives. The framework was applied in a case study in Vietnam where on-site sanitation systems and combined management of human and animal waste were identified as promising interventions.