Molecular fingerprints are one of the most used descriptors in chemoinformatics to compare chemical structures because they can be computed with high efficiency, and by their easy scalability to study large and ultra-large chemical libraries. Molecular fingerprints like MACCS keys and ECFP4 have been used for chemical sampling, visualization, diversity selection, and clustering analysis. These have gained relevance in modern molecular design, especially applied to medicinal chemistry, inorganic chemistry, food chemistry, and in industries such as materials and polymers development, cosmetics, and food industry. In this regard, the traditional molecular design campaign was used to eliminate explicitly metal-base compounds from their large list of chemical candidates to evaluate. This explains that current molecular fingerprints have been developed to analyze organic compounds (e.g., drug-like compounds, natural products, and small peptides). However, other kinds of compounds like metal-based compounds have not been considered during the development of modern molecular fingerprints, at least in part, because of their structural complexity and atomic diversity. Interestingly, the potential of fingerprints to codify the structural properties of metal-based compounds has not been exploited yet. However, there are recent efforts that use basic structural fingerprints, like MACC keys (166 bit), to decode metal-organic frameworks, which has opened new perspectives on the use of this technology in the molecular design area of metal-based compounds. These remarks on the necessity to develop more representative metal-based fingerprints to codify their molecular similarity.