It appears so simple at first glance, “tautomers are isomers of organic compounds that readily interconvert, usually by the migration of hydrogen from one atom to another”. If a chemist can describe the problem so succinctly, one might question why the complication of tautomerism remains a considerable challenge to cheminformatics and computer-assisted drug design. With a half-century of experience with representing molecules in computers, and almost limitless modern computational power, the problem should have been solved by now. The unfortunate answer is that the frustration and inconvenience of a database search failing to find matches due to differences in the tautomeric forms of the query and registered compounds is but the tip of an iceberg. Prototropic tautomerism, the movement of hydrogens around a molecule, is but just one aspect of an interconnected web of complications. These include mesomerism, aromaticity, protonation state, stereochemistry, conformation, polymerization, photostability, hydrolysis, metabolism and EOCWR (explodes on contact with reality). The common theme is that valence theory, which underlies all modern chemical informatics systems, is an approximate theoretical model for representing molecules mathematically, and, as with all models, it has limitations and domains of applicability. In the physical environments that chemists care about, small organic molecules are often dynamic, existing in multiple equivalent or interconvertible forms. A single connection table can at best represent a snapshot or sample from these populations. Although partial algorithmic solutions exist for handling the most common cases of tautomerism, this perspective hopes to argue that the underlying problems perhaps make tautomerism more complex than it might first appear.