Classification is one of the basic tasks of data mining in modern database applications including molecular biology, astronomy, mechanical engineering, medical imaging or meteorology. The underlying models have to consider spatial properties such as shape or extension as well as thematic attributes. We introduce 3D shape histograms as an intuitive and powerful similarity model for 3D objects. Particular flexibility is provided by using quadratic form distance functions in order to account for errors of measurement, sampling, and numerical rounding that all may result in small displacements and rotations of shapes. For query processing, a general filter-refinement architecture is employed that efficiently supports similarity search based on quadratic forms. An experimental evaluation in the context of molecular biology demonstrates both, the high classification accuracy of more than 90% and the good performance of the approach.