In this paper, we introduce a new approach for retrieval and classification of 3D models that directly performs in the Computer-Aided Design (CAD) format without any conversion to other representations like point clouds or meshes, thus avoiding any loss of information. Among the various CAD formats, we consider the widely used STEP extension, which represents a standard for product manufacturing information. This particular format represents a 3D model as a set of primitive elements such as surfaces and vertices linked together. In our approach, we exploit the linked structure of STEP files to create a graph in which the nodes are the primitive elements and the arcs are the connections between them. We then use Graph Neural Networks (GNNs) to solve the problem of model classification. Finally, we created two datasets of 3D models in native CAD format, respectively, by collecting data from the Traceparts model library and from the Configurators software modeling company. We used these datasets to test and compare our approach with respect to state-of-the-art methods that consider other 3D formats. Our code is available at https://github.com/divanoLetto/3D_STEP_Classification CCS Concepts• Computing methodologies → Shape modeling; • Information systems → Information retrieval;