Along with the development of 3D acquisition devices and methods and increasing number of available 3D objects, new tools are necessary to automatically analyze, search and interpret these models. In this paper we describe a novel geometric approach to 3D object comparison and analysis. To compare two objects geometrically we first properly position and align the objects. After solving this pose estimation problem, we generate specific distance histograms that define a measure of geometric similarity of the inspected objects. The geometric approach is very well suited for structures with moderate variance, e.g. bones, fruits, etc. The strength of the approach is proven through results of several tests we performed on different data sets.