In this paper, a methodology to assess the building vulnerability index for a natural disaster is proposed. The building vulnerability index for the census output areas of Gyeongju city, as a representative example, is evaluated for flood hazard to illustrate the proposed methodology. The building vulnerability index, which can be used for flood risk analysis, is measured by combining the following five weighted proxy variables: density of the hazard-exposed area of a building, importance level of a building, type of building's structural material, status of building's structural design, and deterioration level of a building. The selected proxy variables are evaluated using predefined scoring criteria and are then nondimensionalized on the basis of a normalization method. The weight factor for each proxy variable is obtained by analyzing its frequency of use from the flood risk related literature. In addition, building-information databases are established for each census output area to estimate the proxy variables by classifying the raw data of building ledgers by using GIS-related software. The building vulnerability index estimation methodology proposed in this paper can be used to quickly estimate the natural disaster risk for regions composed with the census output areas.