To understand the pathogenesis of a given ion channel disorder, knowledge of the mutation alone is insufficient, instead, the description of the associated functional defect is decisive. The patch clamp technique enables to achieve this both in native tissue as well as heterologous expression systems. By this technique, structure-function relationships of ion channels were elucidated that not only support the homology already suggested by amino acid alignments of different channel types, but that also pointed to regions important for gating, ion selectivity, or subunit interaction. Currently, effort is being made to develop automation of the technique which will result in a cost-effective, fast, and highly accurate method to test for drug actions on high throughput scales. This review contains an overview of channel structures, channel diseases, and methods to study channel function by the patch clamp technique.