We introduce a thoracic cage coordinate system for recording pathology locations in lung CT volume data. The centerlines of each individual rib are extracted and labeled from top to bottom. For each pair of ribs, a three-dimensional ("3D") orthogonal basis is computed by eigen-analysis of the rib centerline points, which are taken as the x, y, and z axes. The rib pairs form a set of reference planes. Therefore, there are a set of coordinate systems (x, y, z), each of which is locally valid between two adjacent planes. To define a location globally, a fourth parameter, n, is added to identify the serial number of the reference plane. The complete coordinate is recorded as (n, x, y, z). This system is robust against deformations due to bending and twisting, and is relatively stable over inhalation. Further, this system may be readily adapted in other 3D modalities, such as MRI volume data.