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Ion channels are transmembrane protein complexes that are found in virtually all cells. They fulfill a crucial physiological function by facilitating communication between and within cells. Consequently, impaired channel function, e.g. due to mutations, often has profound physiological effects. Their central role in cell-to-cell communication makes ion channels formidable drug targets, albeit their transmembrane nature often hampers efforts to obtain high resolution structures and hence impedes drug discovery. Decades of electrophysiology and molecular biology studies have made critical contributions to our understanding of ion channel structure and function. Small organic compounds, acting as either agonist or antagonist, have played vital roles in such studies and in recent years these molecular tools have become more sophisticated. Decorated with fluorescent, photoaffinity and/or affinity tags small molecular tools enable imaging, binding site mapping and isolation of biomolecular targets. Here, some of the methodologies employed in the context of ion channels are discussed and highlighted with representative examples.