In order to incorporate seismic risk of facilities into a decision making framework, procedures are needed to quantify such risk for stakeholders. Seismic loss estimation methods combine seismic hazard, structural response, damage fragility, and damage consequences to allow quantification of seismic risk. This paper presents a loss estimation methodology which provides various measures of seismic risk for a specific facility. The methodology is component-based and can therefore distinguish between different structural configurations or different facility contents and is consistent with state-of-the-art loss assessment procedures. Loss is measured in the forms of direct structural and non-structural repair costs, and although not considered in the example, business disruption and occupant injuries can also be considered. This framework has been packaged in a computer code available for future dissemination in the public domain so that users need only to have a basic understanding of the methodology and the input data that is required. Discussion is given to the flexibility of the framework in terms of the rigour which can be employed at each of the main steps in the procedure. Via a case study of a high-rise office building, the use of the methodology in decision-making is illustrated. Methodological requirements and further research directions are discussed.