Graphein is a python library for constructing graph and surface-mesh representations of protein structures for computational analysis. The library interfaces with popular geometric deep learning libraries: DGL, PyTorch Geometric and PyTorch3D. As feature engineering is a vital step in a machine learning project, the library is designed to be highly flexible, allowing the user to parameterise the graph construction, scalable to facilitate working with large protein complexes,and containing useful pre-processing tools for preparing experimental structure files. Graphein is also designed to facilitate network-based and graph-theoretic analyses of protein structures in a high-throughput manner.