In this work, we developed a methodology to perform a systematic classification based on three-dimensional structural similarity of the metal sites contained in metalloproteins. Our definition of metal site extended beyond the metal ion and its aminoacidic ligands by including all the chemical species (aminoacids, nucleotides, exogenous ligands) providing at least one donor atom as well as all any other chemical species within a radius of 5.0 Å. We previously defined this as the Minimal Functional Site of a metalloprotein (MFS), and showed that its characteristics are related to the metalloprotein function. The methodology described here leverages the MetalS2 algorithm, whose total score provides a quantitative measure of structural similarity between pairs of MFS. We used this measure to build clusters of structurally similar MFSs using a two-stage hierarchical clustering algorithm. At the first stage we cluster MFSs identified in corresponding position within proteins with the same fold. For each of these clusters we then identify a representative MFS. At the second stage, all representative MFSs are clustered. The resulting groups are thus independent of the overall protein fold.