Household biogas digesters are a sustainable technology that can help rural families of low income countries meeting their basic energy needs and improving their standard of living. However, household biogas digester programmes are often promoted without any systematic planning which might help to overcome several challenges for household digesters dissemination (e.g. lack of stakeholders’ involvement, investment cost, technology reliability and durability, lack of site-specific designs). The aim of this study is to develop and validate, for the first time, a multi-criteria decision support tool for the assessment of household biogas digester programmes in rural areas of Latin America. The method is divided into three decision levels. First of all, the rural communities where household digesters may be implemented are evaluated and prioritized. Secondly, the most appropriate digester model (i.e. masonry or plastic tubular digester) is selected. Finally, the most appropriate household digester design (e.g. volume, materials) is identified considering local conditions and beneficiaries’ needs. For that, a set of technical, environmental and socio-economic criteria were defined and weighted by stakeholders at all the decision levels. Furthermore, the tool was validated using three case studies dealing with the implementation of household anaerobic digesters in rural areas of the Peruvian Andes in order to show how it can assist non-profit organizations designing sustainable and successful biogas digester programmes.