Electrical signalling and synaptic transmission in the central nervous system are mediated by the transient activation of different classes of channel proteins which allow for signal propagation along and between excitable cells. Voltage-dependent ion channels control the membrane potential and release of neurotransmitter from presynaptic nerve ending. Ligand-gated ion channels serve as receptors for specific neurotransmitters at peripheral and central synapses. Molecular biology approaches have diclosed primary structures of inhibitory and excitatory neurotransmitter receptor proteins and shown that these belong into a superfamily of evolutionarily related gene products of similar transmembrane topology and quaternary structure. Our laboratory has focused on the investigation of excitatory acetylcholine receptor, glutamate receptor and inhibitory glycine receptor proteins. Structural principles thought to be important for ion conduction through these channels will be discussed. Furthermore, channel proteins have recently have also been disclosed in intracellular membranes including synaptic vesicles. We have analyzed the primary structures of two putative synaptic vesicle channel proteins, synaptophysin and synaptoporin, and discuss the potential role of these channels in the transmitter release process.