The Korean Institute of Science and Technology Information (KISTI) has recently constructed a spinal disease ontology, in cooperation with the Catholic University of Korea, to establish a simulation model to support the diagnosis of age-related spinal disorders. Here we present a web-based three-dimensional (3D) navigation system for this spinal disease ontology to enable users to make more accurate diagnoses of vertebral column diseases by enhanced reasoning capabilities, using a 3D virtual human spine. The navigation system is composed of three main modules: a query module, which retrieves the data from the spinal disease ontology via a web page, a 3D rendering module, which displays a 3D virtual spine using a web browser, and a visualization module that represents the ontological information in response to a query by connecting it with the virtual spine.