Calcium ion channel mutations disrupt channel function and create recognizable disease phenotypes in the nervous system. The broad array of underlying cellular alterations is commensurate with the expanding genetic diversity of the voltage-gated calcium ion channel complex and its critical role in regulating cell function. Currently, 16 calcium channel genes are known, and mutations in 7 of these are associated with distinct inherited neurological disorders. These mutations provide new insight into the structure and function of the channels, and link specific subunits to cellular disease processes, including altered excitability, synaptic signaling, and cell death. Studies of mutant channel behavior, subunit interactions, and the differentiation of neural networks demonstrate unique patterns of downstream rearrangement. Developmental analysis of molecular plasticity in these mutants is a critical step to define the intervening mechanisms that translate aberrant ion channel behavior into the diverse clinical phenotypes observed.